Taxonomy of protists

A modern non-hierarchical interpretation of the phylogeny of eukaryotes, including protists
(the gray unlabeled line next to Sar represents Telonemia)

A protist (/ˈproʊtɪst/) is any eukaryotic organism (one with cells containing a nucleus) that is not an animal, plant, or fungus. The protists do not form a natural group, or clade, since they exclude certain eukaryotes with whom they share a common ancestor;^[a] but, like algae or invertebrates, the grouping is used for convenience. In some systems of biological classification, such as the popular five-kingdom scheme proposed by Robert Whittaker in 1969, the protists make up a kingdom called Protista, composed of "organisms which are unicellular or unicellular-colonial and which form no tissues".^[1][b] In the 21st century, the classification shifted toward a two-kingdom system of protists: Chromista (containing the chromalveolate, rhizarian and hacrobian groups) and Protozoa (containing excavates and all protists more closely related to animals and fungi).^[2]

The following groups contain protists. The clade Opisthokonta also contains the animals and the fungi, and the kingdom Archaeplastida also contains algae and plants.

Symbols and abbreviations used:

nom. cons. — Indicates a conserved name, a name which has been chosen for a taxon despite not being the priority name.

ICZN/ICN — Indicates an ambiregnal taxon that is accepted in both the zoological and the botanical codes of nomenclature, regulated by the ICZN and the ICN respectively.

(P) — Indicates a paraphyletic taxon.

† — Indicates an extinct taxon.

? — Indicates a taxon of uncertain taxonomic position, which may be the case for various reasons, including a lack of genetic data.

→ — Indicates a monotypic relationship.

This article largely follows the efforts of the scientific community and the International Society of Protistologists to revise the taxonomy of protists in a manner that reflects their phylogeny and evolution, striving away from the use of historical paraphyletic taxa and relying exclusively on clades as the basis of the classification. The reference used for the general arrangement of groups is the publication Revisions to the Classification, Nomenclature and Diversity of Eukaryotes, published in 2019 by researcher Sina Adl and coauthors.^[3] Other studies are used for some specific groups of protists that have been revised after 2018, such as slime moulds,^[4] glaucophyte algae,^[5] arcellinid testate amoebae^[6] and planktonic foraminifera.^[7] The usage of higher-level taxon ranks (phylum and kingdom) is unstable, as it varies from one author to the next;^[8][9] as such, said ranks are generally omitted.

The following cladogram shows the relationships between the major groups of protists, as well as the kingdoms of animals, plants and fungi, according to the most recent phylogenetic analyses.^{[10][11][12][13][14][15]}

• Class Thecomonadea^[c] Cavalier-Smith 1993 emend. 2013 → order Apusomonadida Karpov & Mylnikov 1989 → family Apusomonadidae Karpov & Mylnikov 1989. Genera not assigned to a subfamily: Amastigomonas de Saedeleer 1931; Multimonas Cavalier-Smith 2010; Podomonas Cavalier-Smith 2010; Catacumbia Torruella, Galindo et al. 2022; Cavaliersmithia Torruella, Galindo et al. 2022.^[19]
  • Subfamily Apusomonadinae Cavalier-Smith 2010. Genera: Apusomonas Aléxéieff 1924 (=Rostromonas Karpoff & Zhukov 1980); Manchomonas Cavalier-Smith 2010.
  • Subfamily Thecamonadinae Larsen & Patterson 1990. Genera: Chelonemonas Heiss, Lee, Ishida & Simpson 2015; Karpovia Torruella, Galindo et al. 2022; Singekia Torruella, Galindo et al. 2022, Thecamonas Larsen & Patterson 1990.
• Class Breviatea^[c] Cavalier-Smith 2004 → order Breviatida Cavalier-Smith 2004 → family Breviatidae Cavalier-Smith 2013. Genera: Breviata Walker, Dacks & Embley 2006; Lenisia Hamann et al. 2016; Pygsuia Brown et al. 2013; Subulatomonas Katz et al. 2011.

• Nucletmycea Brown et al. 2009 (=Holomycota Liu et al. 2009)
  • Order Rotosphaerida Rainer 1968 (=Cristidiscoidida Page 1987) → family Nucleariidae Cann & Page 1979 (=Pompholyxophridae Page 1987). Genera: Fonticula Worley, Raper & Hohl 1979; Nuclearia Cienkowsky 1865; Parvularia López-Escardó & Torruella 2017; Pompholyxophrys Archer 1869; Lithocolla Schulze 1874; Vampyrellidium^? Zopf 1885; Elaeorhanis^? Greeff 1873; Pinaciophora^? Greeff 1869; Rabdiophrys^? Rainer 1968; Rabdiaster^? Mikrjukov 1999; Thomseniophora^? Nicholls 2013.^[20]
  • Kingdom Fungi R.T. Moore 1980. Excluded from protists.
• Holozoa Lang et al. 2002. Incertae sedis genera: Tunicaraptor Tikhonenkov, Mikhailov, Hehenberger, Karpov, Prokina, Esaulov, Belyakova, Mazei, Mylnikov, Aleoshin & Keeling 2020;^[13] †Bicellum Strother & Wellman 2021.^[21]
  • Class Ichthyosporea^[d] Cavalier-Smith 1998 (=Mesomycetozoea Mendoza et al. 2002)
    • Order Dermocystida Cavalier-Smith 1998 → family Rhinosporidaceae Mendoza et al. 2001. Genera: Amphibiocystidium Pascolini et al. 2003; Amphibiothecum Feldman, Wimsatt & Green 2005; Chromosphaera Grau-Bové et al. 2017; Dermocystidium Pérez 1908; Rhinosporidium Minchin & Fantham 1905; Sphaerothecum Arkush et al. 2003, Valentines Borteiro et al. 2018.^[22]
    • Order Ichthyophonida Cavalier-Smith 1998 (=Ichthyophonae Mendoza et al. 2001) → family Amoebidiidae Reeves 2003. Genera: Abeoforma, Amoebidium, Anurofeca, Astreptonema, Caullerya, Creolimax, Eccrinidus, Enterobryus, Enteropogon, Ichthyophonus, Palavascia, Pseudoperkinsus, Psorospermium, Sphaeroforma.
  • Class Pluriformea^[d] Hehenberger et al. 2017 → order Corallochytrida Cavalier-Smith 1995 emend. 2021^[18]
    • Family Corallochytriidae Cavalier-Smith in Cavalier-Smith & Allsopp 1996. Sole genus: Corallochytrium Raghu-Kumar 1987.
    • Family Syssomonadidae Cavalier-Smith 2021.^[18] Sole genus: Syssomonas Tikhonenkov, Hehenberger, Mylnikov & Keeling 2017.
  • Class Filasterea Shalchian-Tabrizi et al. 2008 → order Ministeriida Cavalier-Smith 1997. Genus not assigned to families: Pigoraptor Tikhonenkov, Hehenberger, Mylnikov & Keeling 2017.
    • Family Ministeriidae Cavalier-Smith 1997. Sole genus: Ministeria Patterson et al. 1993.
    • Family Capsasporidae Cavalier-Smith 1997. Sole genus: Capsaspora Hertel et al. 2002.
    • Family Txikisporidae Urrutia, Feist & Bass 2022. Sole genus: Txikispora Urrutia, Feist & Bass 2022.^[23]
  • Choanozoa Brunet & King 2017^[e]
    • Class Choanoflagellata Kent 1880–1882 (=Craspedomonadina Stein 1878, Craspedomonadaceae Senn 1900, Craspedophyceae Chadefaud 1960, Craspédomonadophycidées Bourrelly 1968, Craspedomonadophyceae Hibberd 1976, Choanomonadea Krylov et al. 1980, Choanoflagelliida Lee, Hutner & Bovee 1985, Choanoflagellatea Cavalier-Smith 1997 emend. Cavalier-Smith 1998, Choanomonada Adl et al. 2005)^[24][25]
      • Order Craspedida Cavalier-Smith 1997, emend. Nitsche et al. 2011 → family Salpingoecidae Kent 1880–1882, emend. sensu Nitsche et al. 2011 (=Codonosigidae Kent 1880–1882). Genera: Astrosiga Kent 1878; Aulomonas Lackey 1942; Barroeca Hake, Burkhardt, Richter & King 2024;^[26] Choanoeca Ellis 1930, Cladospongia M.O.P.Iyengar & K.R.Ramanathan 1940; Codonocladium Stein 1878; Codonosigopsis Senn 1900, Codosiga James-Clark 1866 (=Codonosiga Stein 1878); Desmarella Kent 1878 (=Codonodesmus Stein 1878, Kentrosiga Schiller 1953); Dicraspedella Ellis 1930; Diploeca Ellis 1930; Diplosiga Frenzel 1892; Diplosigopsis Francé 1897; Hartaetosiga Carr, Richter & Nitsche 2017; Kentia Schiller 1953; Lagenoeca Kent 1881; Microstomoeca Carr, Richter & Nitsche 2017; Monosiga Kent 1878; Mylnosiga Carr, Richter & Nitsche 2017; Pachysoeca Ellis 1930; Proterospongia Kent 1882; Salpingoeca James-Clark 1866; Salpingorhiza Klug 1936; Sphaeroeca Lauterborn 1894; Stagondoeca Carr, Richter & Nitsche 2017; Stelexomonas Lackey 1942; Stylochromonas Lackey 1940.
      • Order Acanthoecida Cavalier-Smith 1997, emend. Nitsche et al. 2011
        • Family Acanthoecidae Norris 1965, emend. sensu Nitsche et al. 2011. Genera: Acanthoeca Ellis 1930; Enibas Schiwitza, Arndt & Nitsche 2019;^[27] Helgoeca Leadbeater 2008; Polyoeca Kent 1880; Savillea Loeblich 1967.
        • Family Stephanoecidae Leadbeater 2011. Genera: Acanthocorbis Hara & Takahashi 1984; Amoenoscopa Hara & Takahashi 1987; Apheloecion Thomsen in Thomsen & Boonruang 1983; Bicosta Leadbeater 1978; Calliacantha Leadbeater 1978; Calotheca Thomsen & Moestrup 1983; Campanoeca Throndsen 1974; Campyloacantha Hara & Takahashi 1987; Conion Thomsen 1982; Cosmoeca Thomsen 1984; Crinolina Thomsen 1976; Crucispina Espeland in Espeland & Throndsen 1986; Diaphanoeca Ellis 1929; Didymoeca Doweld 2003; Kakoeca Buck & Marchant in Buck et al. 1990; Monocosta Thomsen 1979; Nannoeca Thomsen 1988; Parvicorbicula Deflandre 1960; Platypleura Thomsen 1983; Pleurasiga Schiller 1925; Polyfibula Manton in Manton & Bremer 1981; Saepicula Leadbeater 1980; Saroeca Thomsen 1979; Spinoeca Thomsen in Thomsen, Østergaard & Hansen 1995; Spiraloecion Marchant & Perrin 1986; Stephanacantha Thomsen in Thomsen & Boonruang 1983; Stephanoeca Ellis 1930; Syndetophyllum Thomsen & Moestrup 1984.
    • Kingdom Metazoa Haeckel 1874, emend. Adl et al. 2005 (=Animalia Linnaeus 1758). Excluded from protists.

• Incertae sedis genera: Belonocystis; Boveella; Biomyxa; Corallomyxa; Gibbodiscus; Hartmannia; Malamoeba; Malpighamoeba; Oscillosignum; Pseudothecamoeba; Rhabdamoeba; Schoutedamoeba; Stereomyxa; Subulamoeba; Triaenamoeba; Unda.^[3]

• Corycidia Kang et al. 2017^[29]
  • Order Trichosida Möbius 1889 → family Trichosphaeriidae Sheehan & Banner 1973 (=Trichosidae Möbius 1889). Sole genus: Trichosphaerium Schneider 1878 (=Atrichosa Cavalier-Smith et al. 2016).
  • Family Microcoryciidae de Saedeleer 1934. Genera: Amphizonella Greeff 1866; Diplochlamys Greeff 1888; Microcorycia^? Cockerell 1911; Parmulina^? Penard 1902 emend. 1909; Penardochlamys^? Deflandre 1953; Zonomyxa^? Nusslin 1882.^[f]
• Subclass Echinamoebia Cavalier-Smith et al. 2016 → order Echinamoebida Cavalier-Smith et al. 2004 emend. Smirnov et al. 2011
  • Family Echinamoebidae Page 1975. Genera: Echinamoeba Page 1975; Micriamoeba Atlan et al. 2012.
  • Family Vermamoebidae Cavalier-Smith & Smirnov 2011. Sole genus: Vermamoeba Cavalier-Smith & Smirnov 2011.
• Elardia Kang et al. 2017^[29]
  • Subclass Leptomyxia Cavalier-Smith et al. 2016 → order Leptomyxida Pussard & Pons 1976 emend. Page 1987
    • Family Leptomyxidae Pussard & Pons 1976. Sole genus: Leptomyxa Goodey 1915 emend. Smirnov et al. 2017.
    • Family Rhizamoebidae Smirnov et al. 2016. Sole genus: Rhizamoeba Page 1972 emend. Smirnov et al. 2017.^[30]
    • Family Flabellulidae Bovee 1970. Sole genus: Flabellula Schaeffer 1926 emend. Tyml, Lisnerová, Kostka & Dyková 2018^[31] (includes Paraflabellula Page & Willumsen 1983).
    • Family Gephyramoebidae Pussard & Pons 1976. Sole genus: Gephyramoeba Goodey 1915.^[30]
  • Superorder Eulobosia Cavalier-Smith et al. 2016
    • Order Arcellinida Kent 1880. Incertae sedis genera: Acipyxis Jung 1942; Apolimia Korganova 1987; Argynnia Vucetich 1974; Armipyxis Dekhtjar 2009; Conicocassis Nasser & Patterson 2015; Cornuapyxis Coûteaux & Chardez 1981; Ellipsopyxella Bonnet 1975; Ellipsopyxis Bonnet 1975; Erugomicula Nasser et al. 2021; Frenopyxis Bobrov & Mazei 2020; Geamphorella Bonnet 1959; Geoplagiopyxis Chardez 1960; Geopyxella Bonnet & Thomas 1955; Hoogenraadia Gauthier-Liévre & Thomas 1958; Jungia Loeblich & Tappan 1961; Lagenodifflugia Medioli & Scott 1983; Lamptopyxis Bonnet 1974; Lamtoquadrula Bonnet 1975; Leptochlamys West 1901; Maghrebia Gauthier-Liévre & Thomas 1958; Meisterfeldia Bobrov 2016; Microquadrula Golemansky 1968; Nabranella Snegovaya & Alekperov 2009; Oopyxis Jung 1942; Paracentropyxis Bonnet 1960; Paraquadrula Deflandre 1932; Pentagonia Gauthier-Liévre & Thomas 1958; Physochila Jung 1942; Planhoogenraadia Bonnet 1977; Pomoriella Golemansky 1970; Pontigulasia Rhumbler 1895; Prantlitina Vašíček & Růžička 1957;^[32] Proplagiopyxis Schönborn 1964; Protoplagiopyxis Bonnet 1962; Protocucurbitella Gauthier-Liévre & Thomas 1960; Pseudawerintzewia Bonnet 1959; Pseudonebela Gauthier-Liévre & Thomas 1953; Schoenbornia Decloître 1964; Sexangularia Awerintzew 1906; Suiadifflugia Green 1975; Trigonopyxis Penard 1912; Wailesella Deflandre 1928;^[6] †Cangwuella K.Wang et al. 2024.^[33]
      • Suborder Phryganellina Bovee 1985
        • Family Phryganellidae Jung 1942. Sole genus: Phryganella Penard 1902.
        • Family Cryptodifflugiidae Jung 1942. Sole genus: Cryptodifflugia Penard 1890.^[34]
      • Suborder Organoconcha Lahr et al. 2019 → family Microchlamyiidae Ogden 1985. Genera: Microchlamys Cockerell 1911 (=Pseudochlamys Claparède & Lachmann 1859); Spumochlamys Kudryavtsev & Hausmann 2007; Pyxidicula Ehrenberg 1838.
      • Suborder Glutinoconcha Lahr et al. 2019
        • Infraorder Volnustoma Lahr et al. 2019 → family Heleoperidae Jung 1942. Genera: Heleopera Leidy 1879; Metaheleopera^? Bartoš 1963.
        • Infraorder Hyalospheniformes Lahr et al. 2019 → family Hyalospheniidae Schultze 1877 emend. Kosakyan et al. 2012. Genera: Alabasta Duckert, Blandenier, Kosakyan & Singer 2018; Alocodera Jung 1942; Apodera Loeblich & Tappan 1961; Certesella Loeblich & Tappan; Cornutheca Kosakyan, Lahr, Mulot, Meisterfeld, Mitchell & Lara 2016; Gibbocarina Kosakyan, Lahr, Mulot, Meisterfeld, Mitchell & Lara 2016; Hyalosphenia (Stein 1857) Schulze 1877; Longinebela Kosakyan, Lahr, Mulot, Meisterfeld, Mitchell & Lara 2016; Mrabella Kosakyan, Lahr, Mulot, Meisterfeld, Mitchell & Lara 2016; Nebela Leidy 1874 emend. Kosakyan, Lahr, Mulot, Meisterfeld, Mitchell & Lara 2016; Padaungiella Lara & Todorov 2012; Planocarina Kosakyan, Lahr, Mulot, Meisterfeld, Mitchell & Lara 2016; Porosia Jung 1942 emend. Bobrov & Kosakyan 2015; Quadrulella Cockerell 1909 emend. Kosakyan, Lahr, Mulot, Meisterfeld, Mitchell & Lara 2016.
        • Infraorder Excentrostoma Lahr et al. 2019 → family Centropyxidae Jung 1942 (includes Plagiopyxidae Bonnet & Thomas 1960). Genera: Awerinzewia Schouteden 1906; Bullinularia Deflandre 1953; Centropyxis Stein 1859; Frenopyxis Bobrov & Mazei 2020;^[35] Golemanskia González-Miguéns, Todorov, Blandenier, Porfirio-Sousa, Ribeiro, Ramos, Lahr & Lara 2022;^[6] Plagiopyxis Penard 1910.
        • Infraorder Cylindrothecina González-Miguéns, Todorov, Blandenier, Porfirio-Sousa, Ribeiro, Ramos, Lahr & Lara 2022 → family Cylindrifflugiidae González-Miguéns, Todorov, Blandenier, Porfirio-Sousa, Ribeiro, Ramos, Lahr & Lara 2022. Sole genus: Cylindrifflugia González-Miguéns, Todorov, Blandenier, Porfirio-Sousa, Ribeiro, Ramos, Lahr & Lara 2022.^[6]
        • Infraorder Longithecina Lahr et al. 2019
          • Family Difflugiidae Wallich 1864. Genera: Difflugia Leclerc 1815, Zivkovicia Ogden 1983.
          • Family Lesquereusiidae Jung 1942. Sole genus: Lesquereusia Schlumberger 1845.
        • Infraorder Sphaerothecina Kosakyan, Lara & Lahr 2016
          • Family Arcellidae Ehrenberg 1843. Genera: Arcella Ehrenberg 1830; Galeripora González-Miguéns et al. 2021.
          • Family Netzeliidae Kosakyan et al. 2016. Genera: Cucurbitella Penard 1902; Cyclopyxis Deflandre 1929; Netzelia Ogden 1979.
    • Order Euamoebida Lepşi 1960 sensu Smirnov et al. 2011^[36]
      • Suborder Amoebina Cavalier-Smith 2016
        • Family Amoebidae Ehrenberg 1838 Page 1987. Genera: Amoeba, Chaos, Polychaos, Parachaos, Trichamoeba, Deuteramoeba, Hydramoeba
        • Family Hartmannellidae Volkonsky 1931. Cashia, Copromyxa, Copromyxella, Glaeseria, Hartmannella, Ptolemeba, Saccamoeba
      • Suborder Nolandina Cavalier-Smith 2016^[36] → family Nolandellidae Cavalier-Smith 2011, Lahr & Katz 2011. Sole genus: Nolandella.

• Class Cutosea Cavalier-Smith 2016 → order Squamocutida Cavalier-Smith 2016
  • Family Squamamoebidae Cavalier-Smith 2016. Genera: Armaparvus Schuler & Brown 2019; Squamamoeba Kudryavtsev & Pawlowski 2013.
  • Family Sapocribridae Cavalier-Smith 2016. Sole genus: Sapocribrum Lahr et al. 2015.
  • Family Idionectidae Hess & Simpson 2019. Sole genus: Idionectes Hess & Simpson 2019.^[37]
• Class Variosea^[g] Cavalier-Smith 2004
  • Angulamoeba Berney, Bass & Geisen 2015
  • Arboramoeba Berney, Bass & Geisen 2015
  • Darbyshirella Berney, Bass & Geisen 2015
  • Dictyamoeba Berney, Bass & Geisen 2015
  • Ischnamoeba Berney, Bass & Geisen 2015
  • Heliamoeba Berney, Bass & Geisen 2015
  • Filamoeba Page 1967
  • Phalansterium Cienkowski 1870.
  • Family Flamellidae Lahr & Katz in Lahr et al. 2011.^[38] Genera included: Flamella Schaeffer 1926; Telaepolella Lahr et al. 2012.
  • Order Protosteliida^ICZN/Protosteliales^ICN L.S.Olive & Stoian. 1966 sensu Shadwick & Spiegel in Adl et al. 2012 → family Protosteliidae^ICZN/Protosteliaceae^ICN L.S.Olive & Stoian. 1966. Sole genus: Protostelium L.S.Olive & Stoian. 1960 (includes Planoprotostelium L.S. Olive & Stoian. 1971).
  • Order Fractovitellida Lahr et al. 2011, sensu Kang et al. 2017
    • Family Acramoebidae Smirnov, Nassonova & Cavalier-Smith 2008. Sole genus: Acramoeba Smirnov, Nassonova & Cavalier-Smith 2008.
    • Family Schizoplasmodiidae Shadwick & Spiegel in Adl et al. 2012. Genera: Ceratiomyxella L.S. Olive & Stoian. 1971; Nematostelium L.S. Olive & Stoian. 1970; Schizoplasmodium L.S. Olive & Stoian. 1966.
    • Family Soliformoviidae Lahr & Katz 2011. Genera: Soliformovum Spiegel 1995; Grellamoeba Dyková, Kostka & Pecková 2008.
  • Order Cavosteliida^ICZN/Cavosteliales^ICN Shadwick & Spiegel in Adl et al. 2012 → family Cavosteliidae^ICZN/Cavosteliaceae^ICN Olive & Stoianovitch 1964. Genera: Cavostelium L.S.Olive 1965; Schizoplasmodiopsis L.S.Olive 1967; Tychosporium Spiegel 1995.
  • Order Holomastigida Lauterborn 1895 (includes Artodiscida Cavalier-Smith 2013) → family Multiciliidae Poche 1913 (includes Artodiscidae Cavalier-Smith 2013). Genera: Artodiscus^? Penard 1890; Multicilia Cienkowsky 1881.
• Class Archamoebea Cavalier-Smith 1983, sensu Cavalier-Smith 2004
  • Family Tricholimacidae Cavalier-Smith 2012. Sole genus: Tricholimax Frenzel 1892.
  • Family Entamoebidae Chatton 1925. Sole genus: Entamoeba Casagrandi & Barbagallo 1895.
  • Family Rhizomastixidae Ptáčková et al. 2013. Sole genus: Rhizomastix Aléxéieff 1911.
  • Order Mastigamoebida Frenzel 1897, sensu Cavalier-Smith 2013.^[h] Genera: Endamoeba Leidy 1879; Endolimax Kuenen & Swellengrebel 1917; Iodamoeba Dobell 1919; Mastigamoeba Schulze 1875; Mastigina Frenzel 1897.
  • Order Pelobiontida Page 1976, sensu Cavalier-Smith 2013 → family Pelomyxidae Schulze 1877. Genera: Mastigella Frenzel 1897; Pelomyxa Greef 1874.
• Superclass Eumycetozoa Zopf 1884 sensu Kang et al. 2017 (=Mycetozoa de Bary 1859 ex Rostafinski 1873, Macromycetozoa Fiore-Donno 2010)
  • Class Dictyostelea^ICZN Lister 1909 sensu Sheikh et al. 2018/Dictyosteliomycetes^ICN Doweld 2001. Genus unassigned to an order: Synstelium S.Baldauf S.Sheikh & Thulin 2018. Incertae sedis genus: Coenonia^? Tiegh. 1884.^[39]
    • Order Acytosteliales S.Baldauf S.Sheikh & Thulin 2018
      • Family Acytosteliaceae Raper ex Raper & Quinlan 1958. Genera: Acytostelium Raper 1956; Rostrostelium S.Baldauf, S.Sheikh & Thulin 2018; Heterostelium S.Baldauf, S.Sheikh & Thulin 2018.
      • Family Cavenderiaceae S.Baldauf, S.Sheikh & Thulin 2018. Sole genus: Cavenderia S.Baldauf, S.Sheikh & Thulin 2018.
    • Order Dictyosteliales L.S.Olive ex P.M.Kirk et al. 2001. Genus unassigned to a family: Coremiostelium S.Baldauf S.Sheikh Thulin & Spiegel 2018.
      • Family Dictyosteliaceae Rostaf. ex Cooke 1877. Genera: Dictyostelium Bref. 1869; Polysphondylium Bref. 1884.
      • Family Raperosteliaceae S.Baldauf S.Sheikh & Thulin 2018. Genera: Hagiwaraea S.Baldauf S.Sheikh & Thulin 2018; Raperostelium S.Baldauf S.Sheikh & Thulin 2018; Speleostelium S.Baldauf S.Sheikh & Thulin 2018; Tieghemostelium S.Baldauf S.Sheikh & Thulin 2018.
  • Class Ceratiomyxea^ICZN/Ceratiomyxomycetes^ICN D. Hawksw., B. Sutton & Ainsw. 2019^[4] → order Protosporangiida^ICZN Shadwick & Spiegel in Adl et al. 2012/Ceratiomyxales^ICN G.W. Martin ex M.L. Farr & Alexop.
    • Family Ceratiomyxidae^ICZN/Ceratiomyxaceae^ICN J.Schröt. 1889. Sole genus: Ceratiomyxa J.Schröt. 1889.
    • Family Protosporangiidae^ICZN Spiegel in Adl et al. 2012/Protosporangiaceae^ICN Leontyev, Stephenson, Schnittler, Shchepin & Novozhilov 2020. Genera: Clastostelium L.S. Olive & Stoian. 1972; Protosporangium L.S. Olive & Stoian. 1972.^[40]
  • Class Myxogastrea^ICZN Cavalier-Smith 1993/Myxomycetes^ICN G.Winter 1880 (=Myxogastres Fr. 1829, Myxogasteres Schröt., 1889, Endosporeae Rostaf. 1873, Myxogastromycetidae G.W.Martin 1961, Myxogastromycetes M.Locquin 1974, Myxogastria Cavalier-Smith 2012 as "Myxogastria L.S.Olive 1970" nom. inval.)^[4]
    • Subclass Lucisporinia^ICZN Cavalier-Smith 2013 as "Lucisporidia"/Lucisporomycetidae^ICN Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019.^[4] Incertae sedis genera: Arcyriatella Hochg. & Gottsb. 1989; Calonema Morgan 1893; Minakatella G.Lister 1921; Trichioides Novozh., Hoof & Jagers 2015.
      • Superorder Cribariidia Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019 → order Cribariida^ICZN/Cribariales^ICN T.Macbr. 1922 → family Cribariidae^ICZN/Cribariaceae^ICN Corda 1838. Genera: Cribaria Pers. 1794; Lindbladia Fr. 1849; Licaethalium Rostaf. 1873.^[4]
      • Superorder Trichiidia Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019^[4]
        • Order Reticulariida^ICZN/Reticulariales^ICN Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019 → family Reticulariidae^ICZN/Reticulariaceae^IZN Chevall. ex Corda 1842. Genera: Alwisia Berk. & Broome 1873 emend. Leontyev, Schnittler, G.Moreno, S.L.Stephenson, D.W.Mitchell & C.Rojas 2014; Lycogala Adans. 1763; Reticularia Bull. 1787–1788; Tubifera J.F.Gmel. 1792 emend. Lentyev, Schnittler & S.L.Stephenson 2015.^[4]
        • Order Liceida^ICZN/Liceales^ICN E. Jahn 1928 → family Liceidae^ICZN/Liceaceae^ICN Chevall. 1826. Genera: Licea Schrad. 1797; Listerella^? E.Jahn 1907.^[4]
        • Order Trichiida^ICZN/Trichiales^ICN T.Macbr. 1922^[4]
          • Family Dianematidae^ICZN/Dianemataceae^ICN T.Macbr. 1922. Genera: Calomyxa Nieuwl. 1916; Dianema Rex. 1891; Dictydiaethalium Rostaf. 1873; Prototrichia Rostaf. 1876.
          • Family Trichiidae^ICZN/Trichiaceae^ICN Chevall. 1826 sensu Martin & Alexopoulos 1969. Genera: Hemitrichia Rostaf. 1873 (includes Trichia decipiens); Arcyria F.H.Wigg. 1780 (includes Arcyodes O.F.Cook 1902); Perichaena^(P) Fr. 1817; Trichia Haller 1768 (includes Cornuvia Rostaf. 1873, Metatrichia Ing 1964, Oligonema Rostaf. 1875).
    • Subclass Columellinia^ICZN Cavalier-Smith 2013 as "Columellidia"/Columellomycetidae^ICN Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019 (=Fuscisporidia Cavalier-Smith 2013 sensu Kretzschmar et al. 2015). Incertae sedis genera: Diachea Fr. 1825; Echinosteliopsis Reinhardt & L.S.Olive 1967; Leptoderma G.Lister 1913; Paradiachea Hertel 1956; Protophysarum M.Blackw. & Alexop. 1975; Trabrooksia H.W.Keller 1980; Willkommlangea Kuntze 1891.^[4]
      • Superorder Echinosteliidia Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019 → order Echinosteliida^ICZN/Echinosteliales^ICN G. W. Martin 1961 → family Echinosteliidae^ICZN/Echinosteliaceae Rostaf. ex Cooke 1877. Genera: Barbeyella Meyl. 1914; Echinostelium de Bary in Rostafiński 1873 (includes Semimorula E.F.Haskins, McGuinn & C.S.Berry 1983).^[4]
      • Superorder Stemonitidia Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019 (=Fuscisporidia Cavalier-Smith 2013 non sensu Kretzschmar et al. 2016)^[4]
        • Order Clastodermatida^ICZN/Clastodermatales^ICN Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019 → family Clastodermatidae^ICZN/Clastodermataceae^ICN Alexop. & T.E. Brooks 1971. Sole genus: Clastoderma A.Blytt 1880.
        • Order Meridermatida^ICZN/Meridermatales^ICN Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019 → family Meridermatidae^ICZN/Meridermataceae^ICN Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019. Sole genus: Meriderma Mar.Mey. & Poulain in Poulain, Meyer & Bozonnet 2011.
        • Order Stemonitida^ICZN/Stemonitidales^ICN T.Macbr. 1922 as "Stemonitales" emend. Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019
          • Family Stemonitidae^ICZN/Stemonitidaceae^ICN Fr. 1829 emend. Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019. Genera: Macbrideola H.C.Gilbert 1934; Stemonitis Gled. 1753; Symphytocarpus Ing & Nann.-Bremek. 1967.
          • Family Amaurochaetidae^ICZN/Amaurochaetaceae ^ICN Rostaf. ex Cooke 1877 emend. Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019. Genera: Comatricha Preuss 1851; Stemonaria Nann.-Bremek., R.Sharma & Y.Yamam. in Nannenga-Bremekamp, Yamamoto & Sharma 1984; Stemonitopsis (Nann.-Bremek.) Nann.-Bremek. 1975; Amaurochaete Rostaf. 1873; Brefeldia Rostaf. 1873; Enerthenema Bowman 1830; Paradiacheopsis Hertel. 1954.
        • Order Physarida^ICZN/Physarales^ICN T.Macbr. 1922. Genus not assigned to a family: Tasmaniomyxa Lloyd et al. 2023.^[41]
          • Family Lamprodermatidae^ICZN/Lamprodermataceae^ICN T.Macbr. 1899 emend. Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019. Genera: Lamproderma Rostaf. (includes Dichaeopsis Meyl. 1930, Colloderma G.Lister 1910, Elaeomyxa Hagelst. 1942); Collaria^(P) Nann.-Bremek. 1967.
          • Family Didymiidae^ICZN/Didymiaceae^ICN Rostaf. ex Cooke 1877. Genera: Diderma Pers. 1794; Didymium Schrad. 1797; Lepidoderma de Bary in Rostafiński 1873; Mucilago Battarra 1755.
          • Family Physaridae^ICZN/Physaraceae^ICN Chevall. 1826. Genera: Craterium Trentep. in Roth 1797; Leocarpus Link 1809; Fuligo Haller 1768; Physarum Pers. 1794 (includes Badhamia Berk. 1852); Physarella Peck. 1882; Physarina Höhn. 1909; Kelleromyxa Eliasson in Eliasson, Keller & Schoknecht 1991.

• Subclass Flabellinia Smirnov et al. 2005. Incertae sedis genera: Microglomus Olive & Stoianovitch 1977; Mycamoeba Blandenier, Seppey, Singer, Vlimant, Simon, Duckert & Lara 2016.^[i][43]
  • Order Stygamoebida^(P) Smirnov & Cavalier-Smith in Smirnov et al. 2011 → family Stygamoebidae Smirnov & Cavalier-Smith in Smirnov et al. 2011. Genera: Stygamoeba Sawyer 1975; Vermistella Moran, Anderson, Dennett, Caron & Gast 2007.^[j]
  • Order Dermamoebida Cavalier-Smith 2004 emend. Kudryavtsev, Voytinsky & Volkova 2022^[44]
    • Family Dermamoebidae Cavalier-Smith & Smirnov 2011. Genera: Dermamoeba Page & Blakey 1979; Paradermamoeba Smirnov & Goodkov 1993; Coronamoeba Kudryavtsev, Voytinsky & Volkova 2022.^[44]
    • Family Mayorellidae Schaeffer 1926. Sole genus: Mayorella Schaeffer 1926.
  • Order Thecamoebida^[h] Schaeffer 1926, sensu Smirnov & Cavalier-Smith 2011. Genera: Sappinia Dangeard 1896; Stenamoeba Smirnov et al. 2007; Stratorugosa Melton & Tekle 2019;^[45] Thecamoeba Fromentel 1874; Thecochaos Page 1981.^[46]
  • Order Dactylopodida^[h] Smirnov et al. 2005 sensu Kang et al. 2017. Genera: Cunea Kudryavtsev & Pawlowski 2015; Janickina^? Chatton 1953; Korotnevella Goodkov 1988; Neoparamoeba Page 1987; Paramoeba Schaudinn 1896; Pseudoparamoeba Page 1979; Vexillifera Schaeffer 1926.
  • Order Vannellida Smirnov et al. 2005 → family Vannellidae Bovee 1979. Genera: Clydonella Sawyer 1975; Lingulamoeba Sawyer 1975; Paravannella Kudryavtsev 2014; Pessonella^? Pussard 1973;^[k] Ripella Smirnov et al. 2007; Vannella Bovee 1965.
• Subclass Centramoebia Cavalier-Smith et al. 2016^[36]
  • Order Acanthopodida^[h] Page 1976 (=Centramoebida Rogerson & Patterson 2002, sensu Tice et al. 2016).^[47] Genera: Acanthamoeba Volkonsky 1931; Balamuthia Visvesvara et al. 1993; Luapeleamoeba Shadwick & Spiegel 2016; Protacanthamoeba Page 1981; Dracoamoeba Tice & Brown 2016; Vacuolamoeba Tice, Geisen & Brown 2016.
  • Order Himatismenida^[h] Page 1987. Genera: Cochliopodium Hertwig & Lesser 1874; Ovalopodium Sawyer 1980; Parvamoeba Rogerson 1993.
  • Order Pellitida^[h] Smirnov & Cavalier-Smith 2011, sensu Kang et al. 2017. Genera: Endostelium L.S.Olive, Bennett & Deasey 1984; Gocevia Valkanov 1932; Paragocevia^? Page 1987; Pellita Smirnov & Kudryavtsev 2005.

• Order Microhelida Cavalier-Smith & Chao in Yabuki et al. 2012 → family Microheliellidae Cavalier-Smith & Chao in Yabuki et al. 2012. Sole genus: Microheliella Cavalier-Smith & Chao in Yabuki et al. 2012.^[l]
• Phylum Telonemia^[m] Shalchian-Tabrizi 2006 → class Telonemea Cavalier-Smith 1993 → order Telonemida Cavalier-Smith 1993 → family Telonemidae Cavalier-Smith 1993. Genera: Arpakorses Tikhonenkov & Karpov 2022;^[48] Lateronema Cavalier-Smith 2015; Telonema Griessmann 1913.

• Division Glaucophyta Skuja 1954 (=Glaucocystaceae West 1904, Glaucocystophyta Kies and Kremer 1986, Glaucoplantae Marin & Melkonian in Li et al. 2020). Incertae sedis genera: Archaeopsis, Chalarodora, Glaucocystopsis, Peliaina, Strobilomonas.^[5]
  • Order Cyanophorales Kies & Kremer 2006. Sole genus: Cyanophora.
  • Order Glaucocystales Bessey 1907. Sole genus: Glaucocystis.
  • Order Gloeochaetales Bessey 1907. Genera: Cyanoptyche, Gloeochaete.
• Phylum Picozoa Seenivasan, Sausen, Medlin & Melkonian 2013 (=picobiliphytes Not et al. 2007) → class Picomonadea Seenivasan, Sausen, Medlin & Melkonian 2013 → order Picomonadida Seenivasan, Sausen, Medlin & Melkonian 2013 → family Picomonadidae Seenivasan, Sausen, Medlin & Melkonian 2013. Sole genus: Picomonas Seenivasan, Sausen, Medlin & Melkonian 2013.^[n]
• Phylum Rhodelphidia Tikhonenkov, Gawryluk, Mylnikov & Keeling 2019 → class Rhodelphidea Tikhonenkov, Gawryluk, Mylnikov & Keeling 2019 → order Rhodelphida Tikhonenkov, Gawryluk, Mylnikov & Keeling 2019 → family Rhodelphidae Tikhonenkov, Gawryluk, Mylnikov & Keeling 2019. Sole genus: Rhodelphis Tikhonenkov, Gawryluk, Mylnikov & Keeling 2019.^[50]
• Division Rhodophyta Wettstein 1901 (=Rhodophyceae Thuret 1855, emend. Rabenhorst 1863, Rhodoplantae Saunders and Hommersand 2004 emend. Adl et al. 2005)

• Division Prasinodermophyta Marin & Melkonian in Li et al. 2020^[51]
  • Class Prasinodermophyceae Marin & Melkonian in Li et al. 2020 → order Prasinodermatales Marin & Melkonian in Li et al. 2020 → family Prasinodermataceae Marin & Melkonian in Li et al. 2020. Sole genus: Prasinoderma Hasegawa & Chihara in Hasegawa et al. 1996.
  • Class Palmophyllophyceae Leliaert et al. 2016 emend. Marin & Melkonian in Li et al. 2020
    • Order Palmophyllales Zechman, Verbruggen, Leliaert, Ashwort, M.A.Buchheim, Fawley, H.Spalding, Pueschel, J.A.Buschheim, Verghese & Hanisak 2010 → family Palmophyllaceae Zechman, Verbruggen, Leliaert, Ashwort, M.A.Buchheim, Fawley, H.Spalding, Pueschel, J.A.Buschheim, Verghese & Hanisak 2010. Genera: Palmophyllum Kützing 1849; Verdigellas Ballantine & Norris 1994; Palmoclathrus^? Womersley 1971.^[52]
    • Order Prasinococcales Guillou et al. ex Leliaert et al. 2016 emend. Marin & Melkonian in Li et al. 2020 → family Prasinococcaceae Leliaert et al. 2016. Sole genus: Prasinococcus Miyashita & Chihara in Miyashita et al. 1993.
• Division Chlorophyta Reichenbach 1828 emend. Pascher 1914 emend. Lewis & McCourt 2004
  • Class Chloropicophyceae Lopes dos Santos & Eikrem 2017 → order Chloropicales Lopes dos Santos & Eikrem 2017 → family Chloropicaceae Lopes dos Santos & Eikrem 2017. Genera: Chloroparvula Lopes dos Santos & Eikrem 2017; Chloropicon Lopes dos Santos & Eikrem 2017.
  • Class Mamiellophyceae Marin & Melkonian 2010
    • Order Mamiellales Moestrup 1984 emend. Marin & Melkonian 2010
      • Family Bathycoccaceae Marin & Melkonian 2010. Genera: Bathycoccus Eikrem & Throndsen 1990; Ostreococcus Courties & Chrétiennot-Dinet 1995.
      • Family Mamiellaceae Moestrup 1984 emend. Marin & Melkonian 2010. Genera: Mamiella Moestrup 1984; Mantoniella Desikachary 1972; Micromonas Manton & Parke 1960.
    • Order Dolichomastigales Marin & Melkonian 2010
      • Family Crustomastigaceae Marin & Melkonian 2010. Sole genus: Crustomastix Nakayama, Kawachi & Inouye 2000.
      • Family Dolichomastigaceae Marin & Melkonian 2010. Sole genus: Dolichomastix Manton 1977.
    • Order Monomastigales R.E.Norris ex Marin & Melkonian 2010 (=Monomastigales Norris in Parker 1982 nomen nudum) → family Monomastigaceae Marin & Melkonian 2010. Sole genus: Monomastix Scherffel 1912.
  • Class Nephroselmidophyceae Cavalier-Smith 1993 emend. Yamaguchi 2011 → order Nephroselmidales Nakayama, Suda, Kawachi & Inouye 2007 → family Nephroselmidaceae Pascher 1913 ex Silva 1980. Genera: Nephroselmis Stein 1878.
  • Class Picocystophyceae Lopes dos Santos & Eikrem 2017 → order Picocystales Lopes dos Santos & Eikrem 2017 → family Picocystaceae Lopes dos Santos & Eikrem 2017. Sole genus: Picocystis R.A.Lewin in Lewin et al. 2000.
  • Class Pseudoscourfieldiophyceae Crépeault, C.Otis, Pombert, Turmel & Lemieu 2024 → order Pseudoscourfieldiales Melkonian 1990 ex Crépeault, C.Otis, Pombert, Turmel & Lemieu 2024 → family Pseudoscourfieldiaceae Melkonian 1990 ex Crépeault, C.Otis, Pombert, Turmel & Lemieu 2024 (=Pycnococcaceae Guillard in Guillard, Keller, O'Kelly & Floyd 1991 emend. M.W.Fawley in Fawley et al. 1999. Sole genus: Pseudoscourfieldia Manton 1975 (=Pycnococcus Guillard in Guillard, Keller, O'Kelly & Floyd 1991).^[53]
  • Class Pyramimonadophyceae Moestrup & Daugbjerg in Daugbjerg et al. 2020^[54] → order Pyramimonadales Chadefaud 1950
    • Family Pyramimonadaceae Korshikov 1938. Genera: Cymbomonas Schiller 1913; Pyramimonas Schmarda 1850; "Prasinopapilla" (not formally described).
    • Family Halosphaeraceae Haeckel 1894. Genera: Halosphaera Schmitz 1878; Pachysphaera Ostenfeld 1899; †Tasmanites^? E.Newton 1875.
  • Core Chlorophyta
    • Class Chlorodendrophyceae Massjuk 2006 → order Chlorodendrales Berger 1954 as "Chlorodendrinales" (=Tetraselmidales Ettl. 1982) → family Chlorodendraceae Oltmanns 1904. Genera: Prasinocladus Kuckuck 1894; Scherffelia Pascher 1912; Tetraselmis Stein 1878.
    • Class Pedinophyceae Moestrup 1991 emend. Fawley, Zechman & Buchheim in Adl et al. 2012^[55]
      • Order Marsupiomonadales Marin 2012
        • Family Marsupiomonadaceae Marin 2012. Sole genus: Marsupiomonas Jones, Leadbeater & Green 1994.
        • Family Resultomonadaceae Marin 2012. Sole genus: Resultomonas Marin 2012.
      • Order Pedinomonadales Moestrup 1991 emend. Marin 2012 → family Pedinomonadaceae Korshikov 1938. Genera: Chlorochytridion Vischer 1945; Pedinomonas Korshikov 1923.
    • UTC clade
      • Class Chlorophyceae Wille 1884
        • SV clade^[56]
          • Order Sphaeropleales^(P?) Luerssen 1877. Incertae sedis genera: Spermatozopsis Korshikov 1913; Golenkinia Chodat 1894; Jenufa Němcová, M.Eliáš, Škaloud & Neustupa 2011; Johansenicoccus.^[57][56][58]
            • Family Dictyochloridaceae Fučíková, P.O.Lewis & L.A.Lewis 2013. Sole genus: Dictyochloris Vischer 1945.
            • Family Sphaeropleaceae Kützing 1849
            • Family Microsporaceae Bohlin 1901
            • Treubarinia. Genera: Trochiscia Kützing 1834; Treubaria C.Bernard 1908; Cylindrocapsa Reinsch 1867; Elakatothrix Wille 1898.^[56]
            • Scenedesminia ("traditional" Sphaeropleales)^[56]
              • Family Bracteacoccaceae P.M.Tsarenko 2005. Sole genus: Bracteacoccus Tereg 1922.
              • Family Bracteamorphaceae Fučíková, P.O.Lewis & L.A.Lewis 2013. Sole genus: Bracteamorpha Fučíková, P.O.Lewis & L.A.Lewis 2013.
              • Family Chromochloridaceae Fučíková, P.O.Lewis & L.A.Lewis 2013. Sole genus: Chromochloris Kol & Chodat 1934.
              • Family Dictyococcaceae^? Fučíková, P.O.Lewis & L.A.Lewis 2013. Sole genus: Dictyococcus Gerneck 1907.
              • Family Hydrodictyaceae Dumortier 1829. Genera: Hydrodictyon Roth; Lacunastrum H.A.McManus; Monactinus Corda; Parapediastrum^(P) E.Hegewald; Pediastrum Meyen.^[59]
              • Family Mychonastaceae Fučíková, P.O.Lewis & L.A.Lewis 2013. Sole genus: Mychonastes P.D.Simpson & S.D.Van Valkenburg 1978.
              • Family Neochloridaceae Ettl & Komárek 1982
              • Family Pseudomuriellaceae Fučíková, P.O.Lewis & L.A.Lewis 2013. Sole genus: Pseudomuriella N.Hanagata 1998.
              • Family Scenedesmaceae Oltmanns 1904
              • Family Schizochlamydaceae Fučíková, P.O.Lewis & L.A.Lewis 2013. Sole genus: Schizochlamys Braun ex Kützing 1849.
              • Family Selenastraceae Blackman & Tansley 1903 (=Ankistrodesmaceae Korshikov 1953)
              • Family Radiococcaceae
              • Family Rotundellaceae Fučíková, P.O.Lewis & L.A.Lewis 2013. Sole genus: Rotundella Fučíková, P.O.Lewis & L.A.Lewis 2013.
              • Family Tumidellaceae Fučíková, P.O.Lewis & L.A.Lewis 2013. Sole genus: Tumidella Fučíková, P.O.Lewis & L.A.Lewis 2013.
          • Order Volvocales Poche 1913
        • OCC clade^[56][58]
          • Order Chaetopeltidales O'Kelly, Watanabe & Floyd
          • Order Chaetophorales Wille 1901
          • Order Oedogoniales Heering 1914
      • Class Trebouxiophyceae Friedl 1995 (=Pleurastrophyceae Mattox et al. 1984)
      • Class Ulvophyceae^(P)
• Division Streptophyta Bremer & Wanntorp 1981 (=Charophyta Migula 1897 emend. Karol et al. 2009)
  • Class Chlorokybophyceae Irisarri et al. 2021 → order Chlorokybales Irisarri et al. 2021 → family Chlorokybaceae Irisarri et al. 2021. Sole genus: Chlorokybus Geitler 1942.^[60]
  • Class Mesostigmatophyceae Marin & Melkonian 1999 emend. Lewis & McCourt 2004 (=Mesostigmata Turmel et al. 2002) → order Mesostigmales Cavalier-Smith 1998 → family Mesostigmataceae Fott 1947. Sole genus: Mesostigma Lauterborn 1894.
  • Class Klebsormidiophyceae C. Jeffrey ex Guiry 2023^[61]
    • Order Klebsormidiales Bierenbroodspot et al. 2024 → family Klebsormidiaceae Bierenbroodspot et al. 2024. Genera: Klebsormidium Silva, Mattox & Blackwell 1972; Interfilum Chodat 1992; Streptofilum Mikhailyuk & Lukešová 2018.
    • Order Entransiales Bierenbroodspot et al. 2024 → family Entransiaceae Bierenbroodspot et al. 2024. Sole genus: Entransia E.O. Hughes 1948.
    • Order Hormidiellales Bierenbroodspot et al. 2024 → family Hormidiellaceae Bierenbroodspot et al. 2024. Genera: Hormidiella Iyengar & Kanthamma 1940; Streptosarcina Mikhailyuk & Lukešová 2018.
  • Phragmoplastophyta Lecointre & Guyander 2006
    • Class Charophyceae Smith 1938 emend. Karol et al. 2009
    • Class Coleochaetophyceae Jeffrey 1982
    • Anydrophyta Rensing 2020^[62]
      • Class Zygnematophyceae van den Hoek et al. 1995 emend. Hall et al. 2009^[63]
        • Order Serritaeniales S.Hess & J.de Vries 2022 → family Serritaeniaceae S.Hess & J.de Vries 2022. Sole genus: Serritaenia A.Busch & S.Hess 2021.
        • Order Zygnematales Bessey 1907 emend. Hess & de Vries 2022 → family Zygnemataceae Kützing 1843. Genera: Cylindrocystis Meneghini 1848; Mesotaenium^? Nägeli 1849; Mougeotia (Roth) C.Agardh 1824; Zygnema C.Agardh 1817 nom. cons.; Zygnemopsis (Skuja) Transeau 1934.
        • Order Desmidiales Bessey 1907 emend. S.Hess & J.de Vries 2022 → family Desmidiaceae Ralfs 1848. Genera: Bambusina Kützing ex Kützing 1849 nom. cons.; Closterium Nitzsch ex Ralfs 1848; Cosmarium Corda ex Ralfs 1848; Cosmocladium Brébisson 1856; Desmidium C.Agardh ex Ralfs 1848; Euastrum Ehrenberg ex Ralfs 1848; Micrasterias C.Agardh ex Ralfs 1848; Netrium (Nägeli) Itzigsohn & Rothe 1856; Nucleotaenium Gontcharov & Melkonian 2010; Onychonema G.C.Wallich 1860; Penium Brébisson ex Ralfs 1848; Phymatodocis Nordstedt 1878; Planotaenium (Ohtani) Petlovany & Palamar-Mordvintseva 2009; Pleurotaenium Nägeli 1849; Staurastrum Meyen ex Ralfs 1848; Staurodesmus Teiling 1948; Xanthidium Ehrenberg ex Ralfs 1848; etc.
        • Order Spirogyrales Clements nom. cons. emend. Hess & de Vries 2022. Sole genus: Spirogyra Link 1820 nom. cons.
      • Kingdom Embryophyta Engler 1886 emend. Lewis & McCourt 2004 (=Plantae Haeckel 1866). Excluded from protists.

• Class Platysulcea Cavalier-Smith 2018 → order Platysulcida Cavalier-Smith 2018 → family Platysulcidae Shiratori, Nakayama & Ishida 2015. Sole genus: Platysulcus Shiratori, Nakayama & Ishida 2015.
• Family Kaonashiidae Weston, Eglit & Simpson 2023. Sole genus: Kaonashia Weston, Eglit & Simpson 2023.^[64]

• Subphylum Opalozoa Cavalier Smith 1991 emend. 2006
  • Infraphylum Placidozoa Cavalier-Smith 2013
    • Class Placididea Moriya, Nakayama & Inouye 2002 → order Placidida Moriya, Nakayama & Inouye 2002 → family Placididae Moriya, Nakayama & Inouye 2002. Genera: Allegra Rybarski & Arndt 2021; Haloplacidia Rybarski, Nitsche & Arndt 2021; Pendulomonas S.M.Tong 1997; Placidia Moriya, Nakayama & Inouye 2002; Placilonga Rybarski & Arndt 2021; Suigetsumonas Okamura & Kondo 2015; Wobblia Moriya, Nakayama & Inouye 2000.^[65]
    • Class Nanomonadea Cavalier-Smith in Cavalier-Smith & Scoble 2013 (=clade MAST-3) → order Uniciliatida Cavalier-Smith in Cavalier-Smith & Scoble 2013
      • Family Incisomonadidae Cavalier-Smith in Cavalier-Smith & Scoble 2013. Sole genus: Incisomonas Scoble & Cavalier-Smith 2013.
      • Family Solenicolidae Cavalier-Smith in Cavalier-Smith & Scoble 2013. Sole genus: Solenicola Pavillard 1916.
    • Class Opalomonadea Cavalier-Smith 2013 (=clade MAST-12). No described species.
    • Superclass Opalinata Wenyon 1926 emend. Cavalier-Smith 1997
      • Class Opalinea Wenyon 1926 (=Slopalinida Patterson 1985)^[66]
        • Order Proteromonadida Grassé 1952 emend. Cavalier-Smith 1993 → family Proteromonadidae Grassé 1952. Sole genus: Proteromonas Kunstler 1883 (= Prowazekella Aléxéieff 1912).
        • Order Opalinida Poche 1913 stat. nov. Hall 1953 emend. Cavalier-Smith
          • Family Karotomorphidae Travis 1934. Sole genus: Karotomorpha Travis 1934.
          • Family Opalinidae Claus 1874. Genera: Cepedea Metcalf 1920; Opalina Purkinje & Valentin 1835; Protoopalina Metcalf 1918; Protozelleriella Delvinquier et al. 1991; Zelleriella Metcalf 1920.
      • Class Blastocystea Zierdt et al. 1967 → order Blastocystida Zierdt 1978 → family Blastocystidae Jiang & He 1988. Sole genus: Blastocystis Alexeieff 1911.
  • Infraphylum Bikosea Cavalier-Smith 2018 (=Bicosoecida Grassé 1926 emend. Karpov 1998) → class Bikosea Cavalier-Smith 1986 as "Bicosoecea" orth. em. 2013. Genera not assigned to families: Bilabrum Schoenle & Arndt in Schoenle et al. 2020;^[67] Cafileria Jirsová, Füssy, Richtová, Gruber, & Oborník 2019;^[68] Cantina Yubuki et al. 2015.
    • Family Pseudobodonidae^? Cavalier-Smith in Cavalier-Smith & Scoble 2013. Sole genus: Pseudobodo Griessmann 1913.^[69]
    • Subclass Rictidia Cavalier-Smith in Cavalier-Smith & Scoble 2013 → order Rictida Cavalier-Smith in Cavalier-Smith & Scoble 2013 → family Rictidae Cavalier-Smith in Cavalier-Smith & Scoble 2013. Sole genus: Rictus Yubuki, Leander & Silberman 2010.
    • Subclass Bicosidia^ICZN/Bicosoecophycidae^ICN Cavalier-Smith in Cavalier-Smith & Chao 2006
      • Superorder Borokiae Cavalier-Smith in Cavalier-Smith & Chao 2006 → order Borokida^ICZN/Borokales^ICN Cavalier-Smith in Cavalier-Smith & Chao 2006 → family Borokidae^ICZN/Borokaceae^ICN Cavalier-Smith in Cavalier-Smith & Chao 2006. Sole genus: Boroka Cavalier-Smith in Cavalier-Smith & Chao 2006.
      • Superorder Cyathobodoniae Cavalier-Smith 1993 emend. 2006. Incertae sedis genus: Halocafeteria Park, Cho & Simpson 2006.^[67]
        • Order Anoecida^ICZN/Anoecales^ICN Cavalier-Smith 1997^[o]
          • Family Anoecidae^ICZN/Anoecaceae^ICN Cavalier-Smith in Cavalier-Smith & Chao 2006. Sole genus: Anoeca Cavalier-Smith in Cavalier-Smith & Chao 2006.
          • Family Caecitellidae^ICZN/Caecitellaceae^ICN Cavalier-Smith in Cavalier-Smith & Chao 2006. Sole genus: Caecitellus Patterson et al. 1993.
          • Family Cafeteriidae^ICZN/Cafeteriaceae^ICN Moestrup 1995. Sole genus: Cafeteria Fenchel & Patterson 1988.
          • Family Symbiomonadaceae Cavalier-Smith in Cavalier-Smith & Chao 2006. Sole genus: Symbiomonas Guillou & Chretiennot-Dinet 1999.
        • Order Bicoecida^ICZN/Bicoecales^ICN Grassé 1926
          • Family Bicosoecidae Stein 1878. Genera: Bicosoeca James-Clark 1866; Stephanocodon Pascher 1942; Poteriodendron.
          • Family Labromonadidae Cavalier-Smith in Cavalier-Smith & Chao 2006. Sole genus: Labromonas Cavalier-Smith in Cavalier-Smith & Chao 2006.
        • Order Pseudodendromonadida^ICZN/Pseudodendromonadales^ICN Hibberd 1985 emend. Cavalier-Smith 2006.
          • Family Pseudodendromonadidae^ICZN/Pseudodendromonadaceae^ICN Karpov 2000. Genera: Cyathobodo Petersen & Hansen 1961; Pseudodendromonas Bourrelly 1953.
          • Family Siluaniidae^ICZN/Siluaniaceae^ICN Karpov 1998. Genera: Adriamonas Verhagen, Zölffel, Brugerolle & D.J.Patterson 1994; Siluania Karpov 1998; Otto Harder, Ekelund & Karpov 2014; Regin Harder, Ekelund & Karpov 2014.^[70]
          • Family Paramonadidae^ICZN/Paramonadaceae^ICN Kent 1880. Sole genus: Paramonas Kent 1881.
          • Family Nanidae^ICZN/Nanaceae^ICN Cavalier-Smith in Cavalier-Smith & Scoble 2013. Sole genus: Nanum Kim et al. 2010 as "Nanos".
          • Family Neradidae^ICZN/Neradaceae^ICN Cavalier-Smith in Cavalier-Smith & Chao 2006. Sole genus: Nerada Cavalier-Smith in Cavalier-Smith & Chao 2006.
          • Family Filidae^ICZN/Filaceae^ICN Cavalier-Smith in Cavalier-Smith & Scoble 2013. Sole genus: Filos Kim et al. 2010.
• Subphylum Sagenista Cavalier-Smith 1995
  • Class Labyrinthulomycetes Arx 1970 ex Dick 2001 (=Labyrinthulea L.S.Olive 1975 ex Cavalier-Smith 1989, 'phylum' Labyrinthomorpha^ICZN Page in Levine et al. 1980/Labyrinthulomycota^ICN Whittaker 1969)^[71]
    • Order Amphitremida (Poche 1913) Gomaa et al. 2013
      • Family Amphitremidae Poche 1913. Genera: Amphitrema; Archerella; Paramphitrema.
      • Family Diplophryidae Cavalier-Smith in Anderson & Cavalier-Smith 2012. Sole genus: Diplophrys Barker 1868.
    • Order Amphifilida Cavalier-Smith in Anderson & Cavalier-Smith 2012 as "Amphifiloidea"
      • Family Amphifilidae Cavalier-Smith in Anderson & Cavalier-Smith 2012. Sole genus: Amphifila Cavalier-Smith in Anderson & Cavalier-Smith 2012.
      • Family Sorodiplophryidae Cavalier-Smith in Anderson & Cavalier-Smith 2012. Genera: Fibrophrys Takahashi, Yoshida, Inouye & Watanabe 2016; Sorodiplophrys Cienkowski 1876.
    • Order Oblongichytrida^ICZN/Oblongichytriales^ICN Bennett et al. 2017 → family Oblongichytriidae^ICZN/Oblongichytriaceae^ICN Cavalier-Smith in Anderson & Cavalier-Smith 2012. Sole genus: Oblongichytrium R.Yokoyama & D.Honda 2006.
    • Order Labyrinthulida^ICZN Doffein 1901/Labyrinthulales^ICN E.A.Bessey 1950
      • Family Aplanochytriidae^ICZN/Aplanochytriaceae^ICN Leander ex Cavalier-Smith in Anderson & Cavalier-Smith 2012. Sole genus: Aplanochytrium Bahnweg & Sparrow 1972 emend. C.A.Leander & D.Porter 2000 (=Labyrinthuloides F.O.Perkins 1973).
      • Family Labyrinthulidae^ICZN Cienkowski 1867/Labyrinthulaceae^ICN Haeckel 1868. Sole genus: Labyrinthula Cienkowski 1864 (=Chlamydomyxa Archer 1875, Pseudoplasmodium Molisch 1926, Labyrinthodictyon Valkanov 1969, Labyrinthorhiza Chadefaud 1956).
      • Family-level clade "Stellarchytriidae^ICZN/Stellarchytriaceae^ICN". Sole genus: Stellarchytrium FioRito & Leander 2016.
    • Order Thraustochytrida^ICZN/Thraustochytriales^ICN Sparrow 1943
      • Family Althorniidae^ICZN/Althornidiaceae^ICN Jones & Alderman 1973. Sole genus: Althornia Jones & Alderman 1971.
      • Family Thraustochytriidae^ICZN/Thraustochytriaceae^ICN Sparrow ex Cejp 1959. Genera: Aurantiochytrium R.Yokoyama & D.Honda 2006; Botryochytrium R.Yokoyama, B.Salleh & D.Honda 2007; Japonochytrium Kobayasi & M.Ookubo 1953; Monorhizochytrium K.Doi & D.Honda 2017; Parietichytrium R.Yokoyama, B.Salleh & D.Honda 2007; Phycophthorum Hassett 2020;^[72] Schizochytrium S.Goldst. & Belsky 1964 emend. R.Yokoyama & D.Honda 2006; Sicyoidochytrium R.Yokoyama, B.Salleh & D.Honda 2007; Thraustochytrium Sparrow 1936 emend. T.W.Johnson in Johnson & Sparrow 1961; Ulkenia A.Gaertn. 1977 emend. R.Yokoyama, B.Salleh & D.Honda 2007.
  • Class Eogyrea Cavalier-Smith 2013 (=clade MAST-6). Genera not assigned to families: Mastreximonas Lax, Cho & Keeling 2024; Vomastromonas Tikhonenkov, Prokina, Cho & Keeling 2024.^[73]
    • Order Eogyrida Cavalier-Smith 2018^[74] → family Pseudophyllomitidae^ICZN/Pseudophyllomitaceae^ICN Shiratori et al. 2017.^[75] Sole genus: Pseudophyllomitus Lee 2002.

• Subphylum Bigyromonada Cavalier-Smith 1998^[76]
  • Class Developea Karpov & Aleoshin 2016 ex Cavalier-Smith 2017 → order Developayellida^ICZN Cavalier-Smith 1987 ex 2017/Developayellales^ICN Doweld 2001 → family Developayellidae^ICZN/Developayellaceae^ICN Cavalier-Smith 1997 ex 2017. Genera: Cubaremonas Tikhonenkov, Cho & Keeling 2022; Develocanicus Tikhonenkov, Cho, Mylnikov & Keeling 2022; Develocauda Tikhonenkov, Cho & Keeling 2022; Developayella Tong 1995; Develorapax Karpov & Aleoshin 2016; Mediocremonas del Campo & Weiler 2020.
  • Class Pirsonea Cavalier-Smith 2017 → order Pirsoniales Cavalier-Smith 1998 emend. Prokina et al. 2024 → Pirsoniaceae Cavalier-Smith 1998 emend. Prokina et al. 2024. Genera: Bordeauxia Prokina et al. 2024; Bullionia Prokina et al. 2024; Feodosia Prokina et al. 2024; Koktebelia Prokina et al. 2024; Noirmoutieria Prokina et al. 2024; Pirsonia Schnepf, Debres & Elbrachter 1990.^[77]
• Subphylum Pseudofungi Cavalier-Smith 1986 (=Heterokontimycotina M.W. Dick 1976, Peronosporomycotina M.W.Dick 2001)^[78]: 288
  • Class Hyphochytrea^ICZN Cavalier-Smith 1986/Hyphochytriomycetes^ICN Sparrow ex M.W.Dick 1983 → order Hyphochytriales Sparrow 1960
    • Family Anisolpidiaceae Karling 1943 emend. Dick 2001. Genera: Anisolpidium Karling 1943; Canteriomyces Sparrow 1960.
    • Family Hyphochytridiomycetaceae Fischer 1892 emend. Karling 1939. Sole genus: Hyphochytrium Karling 1939.
    • Family Rhizidiomycetaceae Karling 1943. Latrostium Zopf 1894; Rhizidiomyces Zopf 1884; Rhizidiomycopsis Sparrow 1960.
  • Class Oomycetes Winter 1897, emend. Dick 1976 (=Peronosporomycetes Dick 2001). Incertae sedis genera: Atkinsiella Vishniac 1958; Ciliatomyces Foissner & Foissner 1995 (=Ciliomyces Foissner & Foissner 1986);^[79] Crypticola Humber et al. 1989; Ectrogella Zopf 1884; Eurychasma Magnus 1905; Halodaphnea M.W.Dick 1998; Haliphthoros Vishniac 1958; Haptoglossa Drechsler 1940; Lagena Vanterp. & Ledingham 1930; Lagenisma Drebes 1968; Olpidiopsis Cornu 1872; Pontisma H.E. Petersen 1905; Pythiella Couch 1935; Rozellopsis Karling 1942; Sirolpidium H.E.Petersen 1905.
    • Saprolegnialean lineage Lara in Adl et al. 2019. Achlya Nees 1823; Aphanomyces de Bary 1860; Aplanopsis Höhnk 1952; Apodachlya Pringsh. 1883; Aquastella S.L.Glockling & D.P. Molloy 2014; Geolegnia Coker & J.V.Harv. 1925; Leptomitus (Roth) C.Agardh 1824; Newbya M.W.Dick & M.A.Spencer 2002; Pythiopsis de Bary 1888; Protoachlya Cocker 1923; Salisapilia Hulvey, Nigrelli, Telle, Lamour & Thines 2010; Saprolegnia Nees 1823; Thraustotheca Humphrey 1893.
    • Peronosporalean lineage Lara in Adl et al. 2019. Albugo (Pers.) Roussel ex Gray 1821; Bremia Regel 1843; Chlamydomyzium M.W.Dick 1997; Halophytopthora H.H.Ho & S.C.Jong 1990; Hyaloperonospora Constant. in Constant. & J.Fatehi 2002; Lagenidium Zopf 1859; Myzocytiopsis M.W.Dick 1997; Peronospora Corda 1837; Plasmopara J.Schröt. 1886; Pythium Pringsh. 1858; Pseudoperonospora Rostovzez 1903; Phytophthora de Bary 1975; Phytopythium Abad, De Cock, Bala, Robideau, A.M.Lodhi & Lévesque in Bala et al. 2010; Pustula Thines 2005.
• Subphylum/Division Ochrophyta Cavalier-Smith 1986, emend. Cavalier-Smith & Chao 1996 (=Heterokontophyta Guiry, R.A.Andersen & Moestrup 2023). Incertae sedis genera: Commation Thomsen & Larsen 1993.^[p]
  • Order Actinophryida^? Claus 1874, emend. Hartmann 1926^[p]
    • Suborder Actinosphaerina Cavalier-Smith 2013 → family Actinosphaeriidae Cavalier-Smith 2013. Sole genus: Actinosphaerium Ritter von Stein 1857 (=Echinosphaerium Hovasse 1965).
    • Suborder Actinophryina Cavalier-Smith 2013
      • Family Actinophryidae Dujardin 1841. Sole genus: Actinophrys Ehrenberg 1830 (=Trichoda Müller 1773 nomen oblitum, Peritricha Bory de St.Vincent 1824 nomen dubium).
      • Family Helioraphidae Cavalier-Smith 2013. Sole genus: Heliorapha Cavalier-Smith 2013.
  • Infraphylum Chrysista Cavalier-Smith 1986. Incertae sedis genera: Chrysoderma C.Billard 1984 nom. inval.; Chrysomeris Carter 1937; Chrysonephos W.R.Taylor 1952; "Giraudyopsis" Dangeard 1965 nom. inval.;^[82] Rhamnochrysis Wilce & Markey 1974.^[q]
    • Class Eustigmatophyceae^? Hibberd & Leedale 1971^[86][r]
      • Clade Goniochloridales K.P.Fawley, M.Eliáš & M.W.Fawley 2013. Genera: Goniochloris Geitler 1928; Pseudostaurastrum Chodat 1921; Tetraedriella Pascher 1930 nom. cons.; Trachydiscus H.Ettl 1964; Trebonskia Přibyl & Procházková 2022;^[88] Vacuoliviride Nakayama, Nakamura, Yokoyama, Shiratori, Inouye & Ishida 2015.
      • Order Eustigmatales Hibberd 1981
        • Paraeustigmatos M.W.Fawley, Nĕmcová & K.P.Fawley 2019^[89]
        • Family Eustigmataceae Hibberd 1981. Genera: Ellipsoidion Pascher 1938; Chlorobotrys Bohlin 1901; Eustigmatos Hibberd 1981; Pseudocharaciopsis K.W.Lee & Bold 1973; Vischeria Pascher 1938.
        • Family Monodopsidaceae Hibberd 1981 (includes Loboceae Hedgewald in Hedgewald, Padisak & Friedl 2007). Genera: Microchloropsis M.W.Fawley, I.Jameson & K.P.Fawley 2015; Monodopsis Hibberd 1981; Nannochloropsis Hibberd 1981; Pseudotetraedriella Hedgewald in Hedgewald, Padisak & Friedl 2007.
        • Family Neomonodaceae R.Amaral, K.P.Fawley, Nĕmcová, T.Ševčíková, Lukešová, M.W.Fawley, L.M.A.Santos & M.Eliáš 2020. Genera: Botryochloropsis^? Preisig & Wilhelm 1989; Characiopsella R.Amaral, K.P.Fawley, Nĕmcová, T.Ševčíková, Lukešová, M.W.Fawley, L.M.A.Santos & M.Eliáš 2020; Munda R.Amaral, K.P.Fawley, Nĕmcová, T.Ševčíková, Lukešová, M.W.Fawley, L.M.A.Santos & M.Eliáš 2020; Neomonodus R.Amaral, K.P.Fawley, Nĕmcová, T.Ševčíková, Lukešová, M.W.Fawley, L.M.A.Santos & M.Eliáš 2020; Pseudellipsoidion (Neustupa & Nĕmcová) Nĕmcová emend. Amaral et al. 2020.
    • SII clade
      • Class Olisthodiscophyceae Barcytė, Eikrem & M. Eliáš 2021 → order Olisthodiscales Cavalier-Smith 2013 emend. Barcytė, Eikrem & M. Eliáš 2021 → family Olisthodiscaceae Cavalier-Smith 2013 emend. Barcytė, Eikrem & M. Eliáš 2021.^[90] Sole genus: Olisthodiscus Carter 1937.
      • Class Pinguiophyceae Kawachi, Inouye, Honda, O'Kelly, Bailey, Bidigare & R.A.Andersen 2002 → order Pinguiochrysidales Kawachi, Inouye, Honda, O'Kelly, Bailey, Bidigare & R.A.Andersen 2002 → family Pinguiochrysidaceae Kawachi, Inouye, Honda, O'Kelly, Bailey, Bidigare & R.A.Andersen 2002. Genera: Glossomastix O'Kelly 2002; Phaeomonas Honda & Inouye 2002; Pinguiochrysis Kawachi 2002; Pinguiococcus R.A.Andersen, D.Potter & J.C.Bailey 2002; Polypodochrysis Magne 1975.
      • SSC clade^[87][81]
        • Chrysophyceae Pascher 1914. Incertae sedis taxa: Chryososaccus, Chrysosphera, Cyclonexis, Lygynion, Phaeoplaca.
          • Chromulinales Pascher 1910. Chromulina, Chrysomonas.
          • Hibberdiales Andersen 1989. Hibberdia.
          • Ochromonadales Pascher 1910. Spumella, Pedospumella, Ochromonas.
          • Paraphysomonadida Scoble & Cavalier-Smith 2014. Paraphysomonas.
          • Synurales Andersen 1987. Chrysodidymus, Mallomonas, Synura, Tesselaria.
        • Picophagea Cavalier-Smith 2006 emend. 2017^[74] [Synchromophyceae S.Horn & C.Wilhelm 2007]. Chlamydomyxa, Chrysopodocystis, Guanochroma, Leukarachnion, Picophagus, Synchroma.
    • SI clade^[85]/PXR clade^[87][81]
      • Class Raphidophyceae Chadefaud 1950 ex Silva 1980 → order Chattonellales Throndsen in Tomas 1993 emend. Yamaguchi, Nakayama, Murakami & Inouye 2010 (=Vacuolariales Shameel, 2001). Genera: Chattonella, Fibrocapsa, Goniostomum, Haramonas, Heterosigma, Merotricha, Vacuolaria.
      • PX clade^[85]
        • Class Chrysoparadoxophyceae Wetherbee in Wetherbee et al. 2019 → order Chrysoparadoxales Wetherbee in Wetherbee et al. 2019 → family Chrysoparadoxaceae Wetherbee in Wetherbee et al. 2019.^[91] Genera: Chrysoparadoxa Wetherbee in Wetherbee et al. 2019; Nematochrysis^? Pascher 1925 (=Chrysowaernella Gayral & Lepailleur 1971).^[85]
        • Phaeophyceae Hansgirg 1886 [Kjellman 1891; Pfitzer 1894]
          • Ascoseirales Petrov 1964. Ascoseira.
          • Desmarestiales Setchell & Gardner 1925. Arthrocladia, Desmarestia (P), Himantothallus, Phaeurus.
          • Dictyotales Bory de Saint-Vincent 1828. Dictyota, Dilophus, Lobophora, Padina, Stypopodium, Taonia, Zonaria.
          • Discosporangiales Kawai et al. 2007. Choristocarpus, Discosporangium.
          • Ectocarpales Bessey 1907, emend. Silva & Reviers 2000. Adenocystis, Acinetospora, Asterocladon, Asteronema, Chordaria, Ectocarpus, Scytosiphon.
          • Fucales Bory de Saint-Vincent 1927. Ascophyllum, Bifurcaria, Cystoseira, Druvillaea, Fucus, Hormosira, Sargassum, Turbinaria.
          • Ishigeales Cho et al. 2004 [Ishigeacea Okamura 1935]. Ishige.
          • Laminariales Migula 1908. Akkesiophycus, Alaria, Chorda, Costaria, Laminaria, Lessonia, Pseudochoda.
          • Nemodermatales Parente et al. 2008. Nemoderma.
          • Onslowiales Draisma & Prud'homme van Reine 2008. Onslowia.
          • Ralfsiales Nakamura ex Lim & Kawai 2007. Lithoderma, Neoralfsia, Pseudolithoderma, Ralfsia.
          • Scytothamnales Peters & Clayton 1998. Scytothamnus, Splachnidium, Stereocladon.
          • Sphacelariales Migula 1908. Chaetopteris, Halopteris, Stypocaulon, Sphacelaria, Verosphacella.
          • Sporochnales Sauvageau 1926. Bellotia, Carpomitra, Nereia, Sporochonus, Tomaculopsis.
          • Syringodermatales Henry 1984. Syringoderma.
          • Tilopteridales Bessey 1907. Cutleria, Halosiphon, Haplospora, Phaeosiphoniella, Phyllaria, Tilopteris.
        • Class Phaeosacciophyceae R.A.Andersen, L.Graf & H.S.Yoon in Graf et al. 2020 → order Phaeosacciales R.A.Andersen, L.Graf & H.S.Yoon in Graf et al. 2020^[85]
          • Family Phaeosaccionaceae J. Feldmann 1949. Genera: Antarctosaccion Delépine 1970; Phaeosaccion Farlow 1882.
          • Family Tetrasporopsidaceae R.A.Andersen, L.Graf & H.S.Yoon in Graf et al. 2020. Genera: Tetrasporopsis Lemmermann 1899; Psammochrysis R.Wetherbee in Graf et al. 2020.
        • Phaeothamniophyceae Andersen & Bailey in Bailey et al. 1998
          • Phaeothamniales Bourrelly 1954, emend. Andersen & Bailey in Bailey et al. 1998. Phaeothamnion.
          • Pleurochloridales Ettl 1956. Pleurochloridella.
        • Schizocladiophyceae Henry, Okuda & Kawai 2003. Schizocladia.
        • Xanthophyceae Allorge 1930, emend. Fritsch 1935 [Heterokontae Luther 1899; Heteromonadea Leedale 1983; Xanthophyta Hibberd 1990]
          • Tribonematales Pascher 1939. Botrydium, Bumilleriopsis, Characiopsis, Chloromeson, Heterococcus, Monadus, Ophiocytium, Sphaerosorus, Tribonema, Xanthonema.
          • Vaucheriales Bohlin 1901. Vaucheria.
  • Diatomista Derelle et al. 2016, emend. Cavalier-Smith 2017 [SIII clade]. Incertae sedis taxa: environmental clades MOCH-1, MOCH-2 and MOCH-4 Massana et al. 2014.
    • Bolidophyceae Guillou et al. 1999 [Parmales Booth & Marchant 1987]. Bolidomonas, Triparma, Tetraparma, Pentalamina.
    • Diatomeae Dumortier 1821 [Bacillariophyta Haeckel 1878]
      • Leptocylindrophytina D.G. Mann, in Adl et al. 2019
        • Leptocylindrophyceae D.G. Mann, in Adl et al. 2019. Leptocylindrus, Tenuicylindrus.
        • Corethrophyceae D.G. Mann, in Adl et al. 2019. Corethron.
      • Ellerbeckiophytina D.G. Mann, in Adl et al. 2019. Ellerbeckia.
      • Probosciophytina D.G. Mann, in Adl et al. 2019. Proboscia.
      • Melosirophytina D.G. Mann, in Adl et al. 2019. Aulacoseira, Melosira, Hyalodiscus, Stephanopyxis, Paralia, Endictya.
      • Coscinodiscophytina Medlin & Kaczmarska 2004, emend. Adl et al. 2019. Actinoptychus, Coscinodiscus, Actinocyclus, Asteromphalus, Aulacodiscus, Stellarima.
      • Rhizosoleniophytina D.G. Mann, in Adl et al. 2019. Guinardia, Rhizosolenia, Pseudosolenia.
      • Arachnoidiscophytina D.G. Mann, in Adl et al. 2019. Arachnoidiscus.
      • Bacillariophytina Medlin & Kaczmarska 2004, emend. Adl et al. 2019
        • Mediophyceae Jouse & Proshkina-Lavrenko in Medlin & Kaczmarska 2004
          • Chaetocerotophycidae Round & R.M. Crawford in Round et al. 1990, emend. Adl et al. 2019. Chaetoceros, Bacteriastrum, Dactyliosolen, Cerataulina, Hemiaulus, Eucampia, Acanthoceras, Urosolenia, Terpsinoë, Hydrosera.
          • Lithodesmiophycidae Round & R.M. Crawford in Round et al. 1990, emend. Adl et al. 2019. Lithodesmium, Lithodesmioides, Helicotheca, Bellerochea, Ditylum.
          • Thalassiosirophycidae Round & R.M. Crawford in Round et al. 1990. Thalassiosira, Lindavia, Cyclotella, Stephanodiscus, Cyclostephanos, Discostella, Bacteriosira, Skeletonema, Detonula.
          • Cymatosirophycidae Round & R.M. Crawford in Round et al. 1990. Cymatosira, Minutocellus, Papiliocellulus, Leyanella, Extubocellulus, Plagiogrammopsis, Campylosira, Brockmanniella, Pierrecomperia.
          • Odontellophycidae D. G. Mann, in Adl et al. 2019. Odontella, Triceratium, Cerataulus, Pleurosira, Pseudauliscus, Amphitetras, Trieres, Mastodiscus.
          • Chrysanthemodiscophycidae D.G. Mann, in Adl et al. 2019. Chrysanthemodiscus, Biddulphiopsis, Trigonium, Isthmia, Lampriscus, Stictocyclus, Ardissonea, Climacosphenia, Toxarium.
        • Biddulphiophyceae D. G. Mann, in Adl et al. 2019
          • Biddulphiophycidae Round and R.M. Crawford in Round et al. 1990, emend. Adl et al. 2019. Biddulphia.
          • Attheya T. West 1860
        • Bacillariophyceae Haeckel 1878, emend. Adl et al. 2019
          • Striatellaceae Kützing 1844. Striatella, Pseudostriatella.
          • Urneidophycidae Medlin 2016. (P?) Plagiogramma, Dimeregramma, Rhaphoneis, Delphineis, Psammoneis, Bleakeleya, Asterionellopsis.
          • Fragilariophycidae Round in Round, Crawford & Mann 1990, emend. Adl et al. 2019. Fragilaria, Synedra, Tabellaria, Asterionella, Diatoma, Tabularia, Cyclophora, Astrosyne, Licmophora, Rhabdonema, Grammatophora, Staurosira, Thalassionema.
          • Bacillariophycidae D.G. Mann in Round, Crawford & Mann 1990, emend. Adl et al. 2019. Eunotia, Achnanthes, Bacillaria, Nitzschia, Pseudonitzschia, Cylindrotheca, Navicula, Seminavis, Haslea, Pleurosigma, Gyrosigma, Achnanthidium, Cocconeis, Frustulia, Diploneis, Sellaphora, Pinnularia, Gomphonema, Cymbella, Didymosphenia, Phaeodactylum, Amphora, Entomoneis, Epithemia, Surirella, etc.
            • Naviculales Bessey 1907
              • Stauroneidaceae D.G. Mann in Round, Crawford & Mann 1990. Craticula, Dorofeyukea, Fistulifera, Karayevia, Madinithidium, Parlibellus, Prestauroneis, Stauroneis, Schizostauron.^[92]
    • Dictyochophyceae Silva 1980 [Silicoflagellata Lemmermann, 1901]
      • Dictyochales Haeckel 1894 [Dictyochida Borgert, 1891; Dictyochaceae Lemmermann, 1901]. Dictyocha.
      • Florenciellales Eikrem, Edvardsen & Throndsen 2007.^[93] Florenciella, Verrucophora.
      • Pedinellales Zimmermann et al. 1984 [Ciliophryida Febre-Chevalier, 1985; Actinomonadaceae Kent, 1880]. Actinomonas, Apedinella, Ciliophrys, Mesopedinella, Palatinella, Pedinella, Pseudopedinella, Pteridomonas.
      • Rhizochromulinales O'Kelly & Wujek 1994 [Rhizochromulinaceae O'Kelly & Wujek, 1994]. Rhizochromulina.
    • Pelagophyceae Andersen & Saunders 1993
      • Pelagomonadales Andersen & Saunders 1993. Aureococcus, Pelagococcus, Pelagomonas.
      • Sarcinochrysidales Gayral & Billard 1977
        • Sarcinochrysidaceae Gayral & Billard 1977. Ankylochrisis, Arachnochrysis, Aureoscheda, Aureoumbra, Nematochrysopsis, Pelagospilus, Pulvinaria, Sarcinochrysis, Sargassococcus.
        • Chrysocystaceae M.Melkonian, H.S.Yoon & R.A.Andersen 2018.^[94] Chrysocystis, Chrysoreinhardia, Sungminbooa.
      • Plocamiomonadales Daugbjerg & Lovejoy 2024. Plocamiomonas.^[95]

• Colponemida^(P) Cavalier-Smith 1993 emend. Adl et al. 2019 (=Protalveolata Cavalier-Smith 1991 emend. 2017. Genera not assigned to families: Neocolponema Gigeroff et al. 2023; Loeffela Gigeroff et al. 2023^[96]
  • Phylum^[s] Colponemidia Tikhonenkov et al. 2014 → class Colponemea Cavalier-Smith 1993 → order Colponemida Cavalier-Smith 1993 → family Colponemidae Cavalier-Smith & Chao 2004. Sole genus: Colponema Stein 1878.
  • Phylum^[s] Acavomonidia Tikhonenkov et al. 2014 → class Acavomonea Tikhonenkov et al. 2014 → order Acavomonida Tikhonenkov et al. 2014 → family Acavomonidae Tikhonenkov et al. 2014. Acavomonas Tikhonenkov et al. 2014.
  • Order Palustrimonadida Cavalier-Smith 2017 → family Palustrimonadidae Cavalier-Smith 2017. Sole genus: Palustrimonas Patterson & Simpson 1996.

• Phylum^[s] Chromerida R.B.Moore et al. 2008 → class Colpodellophyceae Molinari & Guiry 2023^[98] ("chrompodellids")^[99] → order Colpodellales^ICN/Colpodellida^ICZN Cavalier-Smith 1993 emend. Adl et al. 2005, 2019. Incertae sedis genus: Piridium Patten 1936.^[100]
  • Family Vitrellaceae Oborník & Lukeš 2011. Sole genus: Vitrella Oborník & Lukeš 2011.
  • Family Colpodellaceae Adl et al. 2019. Genera: Colpodella Cienkowsky 1865; Chilovora Cavalier-Smith 2004; Voromonas Cavalier-Smith 2004.
  • Family Chromeraceae Oborník & Lukeš 2012. Sole genus: Chromera R.B.Moore et al. 2008.
  • Family Alphamonadaceae^ICN/Alphamonadidae^ICZN Cavalier-Smith in Cavalier-Smith & Chao 2004. Sole genus: Alphamonas Aléxéieff 1918.
• Phylum^[s] Perkinsozoa Norén & Moestrup in Norén et al 1999 → class Perkinsea Levine 1978. Incertae sedis genera: Phagodinium Kristiansen 1993; Rastrimonas Brugerolle 2003;^[t] Acrocoelus Fernández, Pardos, Benito & Arroyo 1999.
  • Maranthos Alacid & Reñé 2021^[105]
  • Family Pararosariidae Jeon & Park 2021. Sole genus: Pararosarium Jeon & Park 2021.^[106]
  • Family Parviluciferaceae Reñé & Alacid 2017. Genera: Dinovorax Reñé & Alacid 2017; Parvilucifera Norén & Moestrup 1999; Snorkelia Reñé & Alacid 2017;^[107] Tuberlatum Jeon & Park 2019.^[108]
  • Family Perkinsidae Levine 1978. Sole genus: Perkinsus Levine 1978.
  • Family Xcellidae Freeman, Fuss, Kristmundsson, Keeling, Shalchian-Tabrizi & Bass 2017 em. Karlsbakk, Nystøyl, Plarre & Nylund 2021. Genera: Cryoxcellia Evans, Patel, Matzke & Millar 2023,^[109] Gadixcellia Freeman, Fuss, Kristmundsson, Keeling, Shalchian-Tabrizi & Bass 2017; Notoxcellia Desvignes et al. 2022;^[110] Salmoxcellia Karlsbakk, Nystøyl, Plarre & Nylund 2021;^[111] Xcellia Freeman, Fuss, Kristmundsson, Keeling, Shalchian-Tabrizi & Bass 2017.
• Phylum^[s] Dinoflagellata Bütschli 1885, emend. Fensome et al. 1993, emend. Adl et al. 2005. Incertae sedis genera: free-living (Adenoides, Akashiwo, Amphidiniella, Ankistrodinium, Apicoporus, Archaeosphaerodiniopsis, Bispinodinium, Bysmatrum, Cabra, Cladopyxis, Crypthecodinium, Cucumeridinium, Dactylodinium, Dicroerisma, Gloeodinium, Grammatodinium, Gynogonadinium, Gyrodiniellum, Halostylodinium, Heterodinium, Moestrupia, Paragymnodinium, Phytodinium, Plagiodinium, Planodinium, Pileidinium, Pseudadenoides, Pseudothecadinium, Pyramidodinium, Rhinodinium, Roscoffia, Sabulodinium, Sphaerodinium, Spiniferodinium, Testudodinium, Thecadinium, Thecadiniopsis, Togula) and parasitic Blastodiniales Chatton 1906 [no longer valid] (Amyloodinium, Apodinium, Cachonella, Caryotoma, Crepidoodinium, Haplozoon, Oodinium, Myxodinium, Piscinoodinium, Protoodinium, Rhinodinium, Schyzochitriodinium, Stylodinium).
  • Psammosa Okamoto, A. Horák & Keeling 2012^[112][113]
  • Family Oxyrrhinaceae Sournia 1984. Sole genus: Oxyrrhis Dujardin 1841.^[113]
  • Eleftheros Tikhonenkov, Hehenberger & Keeling 2023^[113]
  • Class Endodinea Cavalier-Smith 2017 → order Ichthyodinida Cavalier-Smith 2017 (environmental Marine Alveolate Group I)^[113]
    • Family Hobagellidae Yoo, Kim & Wayne Coats 2024. Sole genus: Hobagella Yoo, Kim & Wayne Coats 2024.^[114]
    • Family Euduboscquellidae Coats & Bachvaroff 2012. Euduboscquella D.W.Coats, T.R.Bachvaroff & C.F.Delwiche 2012; Dogelodinium Loeblich & A.R.Loeblich 1966 nom. cons.; Keppenodinium Loeblich & A.R.Loeblich 1966 nom. cons. (=Hollandella Cachon 1964).
    • Family Ichthyodiniidae Cavalier-Smith 2017. Sole genus: Ichthyodinium Hollande & Cachon 1952.
  • Class Ellobiopsea A.R.Loeblich 1976 → order Ellobiopsida Whisler 1990 → family Ellobiopsidae Coutière 1911. Genera: Ellobiopsis Caullery 1910; Thalassomyces Niezabitowski 1913; Parallobiopsis^? B.Collin 1913; Ellobiocystis^? Coutière 1911; Rhizellobiopsis^? Hovasse 1926.^[u]
  • Class Syndiniophyceae^ICN/Syndinea^ICZN A.R.Loeblich 1976 → order Syndiniales A.R.Loeblich 1976
    • Family Amoebophryaceae^ICN/Amoebophryidae^ICZN Cachon 1964 (environmental Marine Alveolate Group II). Sole genus: Amoebophrya Koeppen 1892.
    • Family Syndiniaceae^ICN/Syndinidae^ICZN Chatton 1910 (environmental Marine Alveolate Group IV). Hematodinium, Syndinium, Solenodinium.
    • Family Sphaeriparaceae A.R.Loeblich 1970. Genera: Atlanticellodinium J.Cachon & M.Cachon-Enjumet 1965; Sphaeripara Poche 1911 nom. cons.
  • Class Noctiluciphyceae Fensome et al. 1993→ order Noctilucales Haeckel 1894. Abedinium, Cachonodinium, Craspedotella, Cymbodinium, Kofoidinium, Leptodiscus, Noctiluca, Petalodinium, Pomatodinium, Scaphodinium, Spatulodinium.
  • Class Dinophyceae Pascher 1914
    • Subclass Gymnodiniphycidae Fensome et al. 1993
      • Gymnodiniales F. Stein 1878, emend. G. Hansen & Moestrup in Daugbjerg et al. 2000 sensu stricto. Barrufeta, Chytriodinium, Dissodinium, Erythropsidinium, Greuetodinium, Gymnodinium, Lepidodinium, Nematodinium, Nusuttodinium, Pellucidodinium, Polykrikos, Proterythropsis, Wangodinium,^[116] Warnowia.
      • Amphidinium Claparède & Lachmann 1859, emend. Flø Jørgensen et al. 2004 sensu stricto
      • Gyrodinium Kofoid & Swezy 1921, emend. G. Hansen & Moestrup in Daugbjerg et al. 2000 sensu stricto
      • Kareniaceae Bergholtz et al. 2005. Brachidinium, Karenia, Karlodinium, Takayama.
      • Ceratoperidiniaceae Loeblich III 1980, emend. Reñé & de Salas 2013. Ceratoperidinium, Kirithra.
      • Torodiniales Boutrup, Moestrup & Daugbjerg 2016. Kapelodinium, Torodinium.
      • Levanderina Moestrup et al. 2014
      • Margalefidinium F. Gómez, Richlen & D.M. Anderson 2017
      • Cochlodinium F. Schütt emend. F. Gómez, Richlen & D.M. Anderson 2017 sensu stricto
      • Ptychodiscales Fensome et al. 1993. Achradina, Amphilothus, Balechina, Ptychodiscus, Sclerodinium.
      • Borghiellaceae Moestrup, Lindberg, & Daugbjerg 2009. Baldinia, Borghiella.
      • Tovelliaceae Moestrup et al. 2005. Bernardinium, Esoptrodinium, Jadwigia, Tovellia.
      • Suessiaceae Fensome et al. 1993, emend. Moestrup et al. 2009. Ansanella, Asulcocephalium, Biecheleria, Biecheleriopsis, Leiocephalium, Pelagodinium, Polarella, Prosoaulax, Protodinium, Symbiodinium, Yihiella.
    • Subclass Peridiniphycidae Fensome et al. 1993
      • Gonyaulacales Taylor 1980. Alexandrium, Amylax, Ceratium, Ceratocorys, Coolia, Fukuyoa, Fragilidium, Gambierdiscus, Goniodoma, Gonyaulax, Lingulodinium, Ostreopsis, Pentaplacodinium, Peridiniella, Protoceratium, Pyrocystis, Pyrodinium, Pyrophacus, Tripos.
      • Peridiniales Haeckel 1894. Amphidiniopsis, Archaeperidinium, Blastodinium*, Diplopelta, Diplopsalis, Diplopsalopsis, Herdmania, Niea, Oblea, Palatinus, Parvodinium, Peridinium, Peridiniopsis, Preperidinium, Protoperidinium, Qia, Vulcanodinium.
      • Thoracosphaeraceae Schiller 1930. Aduncodinium, Amyloodinium, Apocalathium, Blastodinium, Chimonodinium, Cryptoperidiniopsis, Duboscquodinium, Ensiculifera, Laciniporus,^[117] Leonella, Luciella, Naiadinium, Paulsenella, Pentapharsodinium, Pfiesteria, Scrippsiella, Stoeckeria, Theleodinium, Thoracosphaera, Tintinnophagus, Tyrannodinium.
      • Podolampadaceae Lindemann 1928. Blepharocysta, Gaarderiella, Heterobractum, Lissodinium, Mysticella, Podolampas.
      • Kryptoperidiniaceae Lindemann 1925 ["dinotoms"]. Blixaea, Durinskia, Galeidinium, Kryptoperidinium, Unruhdinium, etc.
      • Heterocapsaceae Fensome et al. 1993. Heterocapsa.
      • Amphidomataceae Sournia 1984. Amphidoma, Azadinium.
      • Oxytoxaceae Lindemann 1928. Corythodinium, Oxytoxum.
      • Centrodiniaceae Hernández-Becerril 2010. Centrodinium.
    • Dinophysales Kofoid 1926. Amphisolenia, Citharistes, Dinofurcula, Dinophysis, Histioneis, Latifascia, Metadinophysis, Metaphalacroma, Ornithocercus, Oxyphysis, Parahistioneis, Phalacroma, Pseudophalacroma, Sinophysis, Triposolenia.
    • Prorocentrales Lemmermann 1910. Mesoporus, Prorocentrum.
• Class Squirmidea Cavalier-Smith 2014. Digyalum, Filipodium, Platyproteum.^[118][119]
• Phylum^[s] Apicomplexa Levine 1980, emend. Adl et al. 2005. Incertae sedis genera: Aggregata^[v] Frenzel 1885, Christalloidophora Dehorne 1934, Dobellia* Ikeda 1914, Echinococcidium* Porchet 1978, Globidiellum* Brumpt 1913, Joyeuxella* Brasil 1902, Rhabdospora* Laguesse 1906, Spermatobium* Eisen 1895, Spiriopsis* Arvy & Peters 1972, Spirogregarina* Wood & Herman 1943, Toxocystis* Léger & Duboscq 1910, Trophosphaera* Le Calvez 1939.
  • Order Agamococcidiorida^? Levine 1979 (=Histogregarida Cavalier-Smith 2014)
    • Family Gemmocystidae Upton & Peters 1986. Sole genus: Gemmocystis.
    • Family Rhytidocystidae Levine 1979. Sole genus: Rhytidocystis.
  • Order Protococcidiorida^? Kheisin 1956 (=Coelotrophiida Vivier 1982). Angeiocystis*, Coelotropha*, Grellia*, Eleutheroschizon*, Mackinnonia*, Myriosporides*, Myriospora*, Sawayella*.
  • Aconoidasida^(P) Mehlhorn, Peters & Haberkorn 1980 (=Hematozoa Vivier 1982)
    • Order Haemospororida Danielewsky 1885. Dionisia*, Haemocystidium, Haemoproteus, Hepatocystis, Leucocytozoon, Mesnilium*, Nycteria, Parahaemoproteus, Plasmodium, Polychromophilus, Rayella*, Saurocytozoon*.
    • Order Piroplasmida Wenyon 1926. Anthemosoma*, Babesia, Cytauxzoon, Echinozoon*, Haemohormidium*, Sauroplasma*, Serpentoplasma*, Theileria.
    • Order Nephromycida Cavalier-Smith 1993, emend. Adl et al. 2019. Nephromyces, Cardiosporidium.
  • Conoidasida^(P) Levine 1988
    • Order Corallicolida Kwong et al. 2021 → family Corallicolidae Kwong et al. 2021. Genera: Corallicola Kwong et al. 2021; Anthozoaphila Kwong et al. 2021; Gemmocystis Upton & Peters 1986.^[121]
    • Coccidia Leuckart 1879 (P)
      • Suborder Adeleorina Léger 1911. Adelea*, Adelina, Babesiosima*, Bartazoon*, Chagasella*, Cyrilia*, Dactylosoma, Desseria*, Ganapatiella*, Gibbsia*, Haemogregarina, Haemolivia, Hepatozoon, Ithania*, Karyolysus, Klossia, Klossiella*, Legerella*, Orcheobius*, Rasajeyna*.
      • Suborder Eimeriorina Léger 1911. Atoxoplasma, Barrouxia*, Besnoitia, Caryospora, Caryotropha, Choleoeimeria, Cyclospora, Cystoisospora, Defretinella*, Diaspora*, Dorisa*, Dorisiella*, Eimeria, Elleipsisoma*, Goussia, Hammondia, Hyaloklossia, Isospora, Lankesterella, Mantonella*, Merocystis, Neospora, Nephroisospora, Ovivora*, Pfeifferinella, Pseudoklossia, Sarcocystis, Schellackia, Selenococcidium*, Selysina*, Spirocystis*, Toxoplasma, Tyzzeria*, Wenyonella*.
    • Gregarinida Dufour 1828. Incertae sedis taxa: Digyalum Koura et al. 1990, Exoschizon Hukui 1939.
      • Archigregarinorida Grassé 1953 (P). Meroselenidium, Merogregarina, Selenidium, Selenocystis, Veloxidium.
      • Eugregarinorida Léger 1900 (P). Apolocystis*, Amoebogregarina, Ancora, Ascogregarina, Asterophora, Blabericola, Caliculium, Cephaloidophora, Colepismatophila, Cystobia*, Cystocephalus*, Difficilina, Diplauxis*, Enterocystis, Ganymedes, Geneiorhynchus, Gonospora, Gregarina, Heliospora, Hentschelia*, Hirmocystis*, Hoplorhynchus, Lankesteria, Lecudina, Leidyana, Lithocystis, Monocystella*, Monocystis, Nematopsis, Nematocystis*, Neoasterophora*, Paralecudina, Paraschneideria, Phyllochaetopterus, Pileocephalus*, Polyplicarium, Polyrhabdina, Porospora*, Prismatospora, Protomagalhaensia, Psychodiella, Pterospora, Pyxinia, Pyxinioides, Rhabdocystis*, Sphaerorhynchus*, Steinina, Stenophora, Stylocephalus, Sycia*, Syncystis, Thalicola*, Thiriotia, Trichotokara, Uradiophora*, Urospora, Xiphocephalus, Zygosoma*, and more.
      • Neogregarinorida Grassé 1953. Apicystis, Aranciocystis, Caulleryella*, Coelogregarina*, Farinocystis*, Gigaductus*, Lipocystis*, Lipotropha*, Lymphotropha*, Machadoella*, Mattesia, Menzbieria, Ophryocystis, Schizocystis*, Syncystis, Tipulocystis*.
      • Cryptogregarinorida Cavalier-Smith 2014, emend. Adl et al. 2019. Cryptosporidium.
    • Class Blastogregarinea Chatton and Villeneuve 1936, emend. Simdyanov et al. 2018. Chattonaria, Siedleckia.

• Postciliodesmatophora Gerassimova & Seravin 1976
  • Karyorelictea Corliss 1974
    • Kentrophoridae Jankowski 1980. Kentrophoros.
    • Loxodida Jankowski 1980
      • Cryptopharyngidae Jankowski 1980. Cryptopharynx.
      • Loxodidae Bütschli 1889. Loxodes.
    • Geleiidae Kahl 1933. Geleia.
  • Heterotrichea Stein 1859
    • Blepharismidae Jankowski in Small & Lynn 1985. Blepharisma
    • Climacostomidae Repak 1972. Climacostomum.
    • Condylostomatidae Kahl in Doflein & Reichenow 1929. Chattonidium, Condylostoma.
    • Fabreidae Shazib et al. 2014. Fabrea.
    • Gruberiidae Shazib et al. 2014. Gruberia.
    • Coliphorina Jankowski 1967
      • Folliculinidae Dons 1914. Folliculina.
      • Maristentoridae Miao et al. 2005. Maristentor.
    • Peritromidae Stein 1867. Peritromus.
    • Spirostomidae Stein 1867. Anigsteinia, Spirostomum.
    • Stentoridae Carus 1863. Stentor.
• Intramacronucleata Lynn 1996. Incertae sedis taxa: Protocruziidae Jankowski 1980 [Protocruziidia de Puytorac et al. 1987] (Protocruzia Faria da Cunha & Pinto 1922).
  • SAL Gentekaki et al. 2014. Incertae sedis taxa: Cariacotrichea Orsi et al. 2011 (Cariacothrix caudata), Mesodiniidae ankowski, 1980 (Mesodinium), Phacodiniidia Small and Lynn 1985 (Phacodinium).
    • Spirotrichea Bütschli 1889
      • Euplotia Jankowski 1979
        • Euplotida Small & Lynn 1985
          • Aspidiscidae Ehrenberg 1830. Aspidisca.
          • Certesiidae Borror & Hill 1995. Certesia.
          • Euplotidae Ehrenberg 1838. Euplotes.
          • Gastrocirrhidae Fauré-Fremiet 1961. Gastrocirrhus.
          • Uronychidae Jankowski 1975. Diophrys, Uronychia.
        • Discocephalida
          • Discocephalidae Jankowski 1979. Discocephalus, Prodiscocephalus, Paradiscocephalus.
          • Pseudoamphisiellidae Song et al. 1997. Leptoamphisiella, Pseudoamphisiella.
      • Perilemmaphora Berger 2008
        • Hypotrichia Stein 1859
          • Stichotrichida Fauré-Fremiet 1961 (P)^[w]
            • Amphisiellidae Jankowski 1979. Amphisiella, Bistichella.
            • Atractosidae Bourland 2015. Atractos.
            • Epiclintidae Wicklow & Borror 1990. Epiclintes.
            • Gonostomatidae Small & Lynn 1985. Cotterillia, Gonostomum.
            • Halteriidae Claparède & Lachmann 1858. Halteria, Meseres.
            • Holostichidae Fauré-Fremiet 1961. Holosticha, Uncinata.
            • Kahliellidae Tuffrau 1979. Deviata, Kahliella.
            • Keronidae Dujardin 1840. Kerona.
            • Oxytrichidae Ehrenberg 1830 (P). Cyrtohymena, Gastrostyla, Oxytricha, Stylonychia.
            • Parabirojimidae Dai & Xu 2011. Parabirojimia, Tunicothrix.
            • Plagiotomidae Bütschli 1887. Plagiotoma.
            • Psammomitridae Jankowski 1979. Psammomitra.
            • Pseudoamphisiellidae Song et al. 1996. Pseudoamphisiella.
            • Psilotrichidae Bütschli 1889. Psilotricha, Urospinula.
            • Schmidingerotrichidae Foissner 2012. Schmidingerothrix.
            • Spirofilidae von Gelei 1929. Spirofilopsis, Strongylidium.
            • Trachelostylidae Small & Lynn 1985. Trachelostyla.
            • Uroleptidae Foissner & Stoeck 2008. Paruroleptus, Uroleptus.
          • Urostylida Jankowski 1979 (P)
            • Bergeriellidae Liu et al. 2010. Bergeriella, Neourostylopsis.
            • Hemicycliostylidae Lyu et al. 2018. Australothrix, Hemicycliostyla.
            • Pseudokeronopsidae Borror & Wicklow, 1983. Apoholosticha, Pseudokeronopsis.
            • Pseudourostylidae Jankowski 1979. Pseudourostyla.
            • Urostylidae Bütschli 1889. Bakuella, Diaxonella, Urostyla.
        • Oligotrichea Bütschli 1887
          • Oligotrichida Bütschli 1887
            • Cyrtostrombidiidae Agatha 2004. Cyrtostrombidium.
            • Pelagostrombidiidae Agatha 2004. Pelagostrombidium.
            • Strombidiidae Fauré-Fremiet 1970. Strombidium (P).
            • Tontoniidae Agatha 2004. Laboea, Tontonia.
          • Choreotrichida Small & Lynn 1985. Incertae sedis taxa: Lynnella Liu et al. 2011 [Lynnellidae Liu et al. 2011; Lynnellida Liu et al. 2015]
            • Strobilidiina Jankowski 1980 (P)
              • Leegaardiellidae Lynn & Montagnes 1988. Leegaardiella.
              • Lohmanniellidae Montagnes & Lynn 1991. Lohmanniella.
              • Strobilidiidae Kahl in Doflein & Reichenow 1929. Strobilidium.
              • Strombidinopsidae Small & Lynn 1985. Strombidinopsis (P).
            • Tintinnina Kofoid & Campbell 1929. Incertae sedis taxa: Helicostomella, Tintinnopsis (P), several other genera.
              • Ascampbelliellidae Corliss 1960. Ascampbelliella
              • Cyttarocylididae Kofoid & Campbell 1929 [probably synonymous with Petalotrichidae]. Cyttarocylis.
              • Dictyocystidae Haeckel 1873. Dictyocysta.
              • Epiplocylididae Kofoid & Campbell 1939. Epiplocylis.
              • Eutintinnidae Bachy et al. 2012. Dartintinnus, Eutintinnus.
              • Favellidae Kofoid & Campbell 1929. Favella.
              • Nolaclusiliidae Sniezek et al. 1991. Nolaclusilis.
              • Petalotrichidae Kofoid & Campbell 1929 [probably synonymous with Cyttarocylididae]. Petalotricha.
              • Ptychocylididae Kofoid & Campbell 1929. Cymatocylis, Ptychocylis.
              • Rhabdonellidae Kofoid & Campbell 1929. Metacylis, Rhabdonella, Schmidingerella.
              • Stenosemellidae Campbell 1954 (P). Stenosemella.
              • Tintinnidae Claparède & Lachmann 1858. Amphorellopsis, Salpingacantha, Salpingella, Tintinnus.
              • Tintinnidiidae Kofoid & Campbell 1929. Tintinnidium.
              • Undellidae Kofoid & Campbell 1929. Undella.
              • Xystonellidae Kofoid & Campbell 1929. Dadayiella, Parafavella, Xystonella.
      • Licnophoridae Bütschli 1887. Licnophora, Prolicnophora.
      • Kiitrichidae Nozawa 1941. Caryotricha, Kiitricha.
    • Lamellicorticata Vd'ačný et al. 2010
      • Armophorea Lynn 2004. Incertae sedis taxa: Mylestomatidae Kahl in Doflein & Reichenow, 1929 (Mylestoma).
        • Metopida Jankowski 1980 (P)
          • Metopidae Kahl 1927 (P). Bothrostoma, Brachonella, Eometopus, Metopus, Parametopidium, Tesnospira.
          • Apometopidae Foissner 2016. Cirranter, Urostomides.
          • Tropidoatractidae Rotterová et al. 2018. Palmarella, Tropidoatractus.
        • Clevelandellida de Puytorac & Grain 1976
          • Clevelandellidae Kidder 1938. Clevelandella.
          • Inferostomatidae Ky 1971. Inferostoma.
          • Neonyctotheridae Affa'a 1987. Neonyctotherus.
          • Nyctotheridae Amaro 1972 (P). Nyctotherus.
          • Sicuophoridae Amaro 1972. Sicuophora.
        • Caenomorphidae Poche 1913. Caenomorpha, Ludio, Sulfonecta.
        • Odontostomatida Sawaya 1940
          • Discomorphellidae Corliss 1960. Discomorphella.
          • Epalxellidae Corliss 1960. Epalxella, Saprodinium.
      • Litostomatea Small & Lynn 1981
        • Rhynchostomatia Jankowski 1980
          • Dileptida Jankowski 1978
            • Dileptidae Jankowski 1980. Apodileptus, Dileptus, Pseudomonilicaryon.
            • Dimacrocaryonidae Jankowski 1978. Dimacrocaryon, Monomacrocaryon, Rimaleptus.
            • Tracheliidae Ehrenberg 1838. Trachelius.
        • Haptoria Corliss 1974 (P). Incertae sedis taxa: Chaenea.
          • Lacrymariidae de Fromentel 1876. Lacrymaria.
          • Haptorida Corliss 1974
            • Enchelyodonidae Foissner et al. 2002. Enchelyodon, Fuscheria.
            • Homalozoonidae Jankowski 1980. Homalozoon.
            • Pleuroplitidae Foissner 1996. Pleuroplites.
          • Didiniidae Poche 1913. Didinium, Monodinium.
          • Pleurostomatida Schewiakoff 1896
            • Amphileptidae Bütschli 1889. Amphileptus.
            • Litonotidae Kent 1882. Litonotus.
            • Kentrophyllidae Wu et al. 2015. Epiphyllum, Kentrophyllum.
          • Spathidiida Foissner & Foissner 1988
            • Acropisthiidae Foissner & Foissner 1988. Acropisthium, Chaenea.
            • Actinobolinidae Kahl 1930. Actinobolina.
            • Apertospathulidae Foissner et al. 2005. Apertospathula.
            • Enchelyidae Ehrenberg 1838. Enchelys.
            • Pseudoholophryidae Berger et al. 1984. Pseudoholophrya.
            • Spathidiidae Kahl in Doflein & Reichenow 1929. Legendrea,^[122] Spathidium.
            • Trachelophyllidae Kent 1882. Trachelophyllum.
          • Helicoprorodontidae Small & Lynn 1985
        • Trichostomatia Bütschli 1889
          • Vestibuliferida de Puytorac et al. 1974
            • Balantidiidae Reichenow in Doflein and Reichenow 1929. Balantidium, Neobalantidium (P).
            • Buetschliidae Poche 1913. Buetschlia.
            • Paraisotrichidae da Cunha 1917. Paraisotrichia.
            • Protocaviellidae Grain in Corliss 1979. Protocaviella.
            • Protohalliidae da Cunha & Muniz 1927. Protohallia.
            • Pycnotrichidae Poche 1913. Pycnothrix, perhaps Buxtonella.
        • Isoendo
          • Isotrichidae Bütschli 1889. Dasytricha, Isotricha.
          • Entodiniomorphida Reichenow in Doflein & Reichenow 1929
            • Blepharocorythina Wolska 1971
              • Blepharocorythidae Hsiung 1929. Blepharocorys.
              • Parentodiniidae Ito, Miyazaki & Imai 2002. Parentodinium.
              • Pseudoentodiniidae Wolska 1986. Pseudoentodinium.
            • Entodiniomorphina Reichenow in Doflein & Reichenow 1929
              • Cycloposthiidae Poche 1913. Cycloposthium.
              • Gilchristinidae Ito, Ishihara & Imai 2014 [Gilchristidae Ito et al. 2006]. Digilchristia, Gilchristina.^[123]
              • Ophryoscolecidae Stein 1859. Entodinium, Ophryoscolex, Polyplastron.
              • Polydiniellidae Corliss 1960. Polydiniella.
              • Rhinozetidae Van Hoven, Gilchrist & Hamilton-Attwell 1988. Rhinozeta.
              • Spirodiniidae Strelkow 1939. Spirodinium.
              • Telamodiniidae Latteur & Dufey 1967. Telamodinium.
              • Troglodytellidae Corliss 1979. Troglodytella,.
          • Macropodiniida Lynn 2008
            • Amylovoracidae Cameron & O'Donoghue 2002. Amylovorax.
            • Macropodiniidae Dehority 1996. Macropodinium.
            • Polycostidae Cameron & O'Donoghue 2003. Polycosta.
  • CONTHREEP Lynn in Adl et al. 2012 [Ventrata Cavalier-Smith 2004]. Incertae sedis taxa: Askenasia Blochmann 1895, Cyclotrichiidae Jankowski 1980 (Cyclotrichium), Paraspathidium Noland 1937, Pseudotrachelocercidae Song 1990 (Pseudotrachelocerca), Discotrichidae Jankowski 1967 [Discotrichida Fan et al. 2014] (Discotricha, Lopezoterenia).
    • Phyllopharyngea de Puytorac et al. 1974
      • Synhymeniida de Puytorac et al. in Deroux 1978
        • Nassulopsidae Deroux in Corliss 1979. Nassulopsis.
        • Orthodonellidae Jankowski 1968. Orthodonella, Zosterodasys.
        • Scaphidiodontidae Deroux in Corliss 1979. Chilodontopsis, Scaphidiodon.
        • Synhymeniidae Jankowski in Small & Lynn 1985. Synhymenia.
      • Subkinetalia Gong et al. 2009
        • Cyrtophoria Fauré-Fremiet in Corliss 1956
          • Chlamydodontida Deroux 1976 (P)
            • Chilodonellidae Deroux 1970. Chilodonella.
            • Chitonellidae Small & Lynn 1985. Chitonella.
            • Chlamydodontidae Stein 1859. Chlamydodon.
            • Gastronautidae Deroux 1994. Gastronauta.
            • Kryoprorodontidae Alekperov & Mamajeva 1992. Gymnozoum.
            • Lynchellidae Jankowski 1968. Chlamydonella, Lynchella.
          • Dysteriida Deroux 1976
            • Dysteriidae Claparède & Lachmann 1858. Dysteria (P), Trochilia.
            • Hartmannulidae Poche 1913 (P). Hartmannula.
            • Kyaroikeidae Sniezek & Coats 1996. Kyaroikeus.
            • Plesiotrichopidae Deroux 1976. Plesiotrichopus.
            • Chonotrichia Wallengren 1895
              • Exogemmida Jankowski 1972
                • Chilodochonidae Wallengren 1895. Chilodochona.
                • Filichonidae Jankowski 1973. Filichona.
                • Helichonidae Jankowski 1972. Heliochona.
                • Lobochonidae Jankowski 1967. Lobochona.
                • Phyllochonidae Jankowski 1972. Phyllochona.
                • Spirochonidae Stein 1854. Spirochona.
              • Cryptogemmida Jankowski 1975
                • Actinichonidae Jankowski 1973. Actinichona.
                • Echinichonidae Jankowski 1973. Echinichona.
                • Inversochonidae Jankowski 1973. Inversochona.
                • Isochonidae Jankowski 1973. Isochona.
                • Isochonopsidae Batisse & Crumeyrolle 1988. Isochonopsis.
                • Stylochonidae Mohr 1948. Stylochona.
        • Rhynchodia Chatton & Lwoff 1939
          • Hypocomidae Bütschli 1889. Hypocoma.
          • Rhynchodida Chatton & Lwoff 1939
            • Ancistrocomidae Chatton & Lwoff 1939. Ancistrocoma.
            • Sphenophryidae Chatton & Lwoff 1921. Sphenophrya.
        • Suctoria Claparède & Lachmann 1858
          • Exogenida Collin 1912
            • Allantosomatidae Jankowski 1967. Allantosoma.
            • Dentacinetidae Batisse 1992. Dentacineta.
            • Dendrosomididae Jankowski 1978. Dendrosomides.
            • Ephelotidae Kent 1882. Ephelota.
            • Lecanophryidae Jankowski 1973. Lecanophrya.
            • Manuelophryidae Dovgal 2002. Manuelophrya.
            • Metacinetidae Bütschli 1889. Metacineta.
            • Ophryodendridae Stein 1867. Ophryodendron.
            • Paracinetidae Jankowski 1978. Paracineta.
            • Phalacrocleptidae Kozloff 1966. Phalacrocleptes.
            • Podophryidae Haeckel 1866. Podophrya.
            • Praethecacinetidae Dovgal 1996. Praethecacineta.
            • Rhabdophryidae Jankowski 1970. Rhabdophrya.
            • Severonidae Jankowski 1981. Severonis.
            • Spelaeophryidae Jankowski in Batisse 1975. Spelaeophrya.
            • Tachyblastonidae Grell 1950. Tachyblaston.
            • Thecacinetidae Matthes 1956. Thecacineta.
          • Endogenida Collin 1912
            • Acinetidae Stein 1859. Acineta.
            • Acinetopsidae Jankowski 1978. Acinetopsis.
            • Choanophryidae Dovgal 2002. Choanophrya.
            • Corynophryidae Jankowski 1981. Corynophrya.
            • Dactylostomatidae Jankowski 1978. Dactylostoma.
            • Dendrosomatidae Fraipont 1878. Dendrosoma.
            • Endosphaeridae Jankowski in Corliss 1979. Endosphaera.
            • Erastophryidae Jankowski 1978. Erastophrya.
            • Pseudogemmidae Jankowski 1978. Pseudogemma.
            • Rhynchetidae Jankowski 1978. Rhyncheta.
            • Solenophryidae Jankowski 1981. Solenophrya.
            • Tokophryidae Jankowski in Small & Lynn 1985. Tokophrya.
            • Trichophryidae Fraipont 1878. Trichophrya.
          • Evaginogenida Jankowski in Corliss 1979
            • Cometodendridae Jankowski 1978. Cometodendron.
            • Cyathodiniidae da Cuhna 1914. Cyathodinium.
            • Dendrocometidae Haeckel 1866. Dendrocometes.
            • Discophryidae Collin 1912. Discophrya.
            • Enchelyomorphidae Augustin & Foissner 1992. Enchelyomorpha.
            • Heliophryidae Corliss 1979. Heliophrya.
            • Periacinetidae Jankowski 1978. Periacineta.
            • Prodiscophryidae Jankowski 1978. Prodiscophrya.
            • Rhynchophryidae Jankowski 1978. Rhynchophrya.
            • Stylocometidae Jankowski 1978. Stylocometes.
            • Trypanococcidae Dovgal 2002. Trypanococcus.
    • Colpodea Small & Lynn 1981
      • Bursariomorphida Fernández-Galiano 1978
        • Bryometopidae Jankowski 1980. Bryometopus (P), Thylakidium.
        • Bursaridiidae Foissner 1993. Bursaridium, Paracondylostoma.
        • Bursariidae Bory de St. Vincent 1826. Bursaria.
      • Colpodida de Puytorac et al. 1974. Incertae sedis taxa: Bardeliellidae Foissner 1984 (Bardeliella), Hausmanniellidae Foissner 1987 (Avestina, Hausmanniella), Ilsiellidae Bourland et al. 2011 (Ilsiella), Pseudochlamydonellidae Buitkamp et al. 1989 (Hackenbergia, Pseudochlamydonella) and Marynidae Poche 1913 (Maryna).
        • Bryophryina de Puytorac et al. 1979
          • Bryophryidae de Puytorac et al. 1979. Bryophrya.
          • Sandmanniellidae Foissner & Stoeck 2009. Sandmanniella.
        • Colpodina Foissner et al. 2011
          • Colpodidae Bory de St. Vincent 1826 (P). Colpoda.
          • Grandoriidae Corliss 1960. Grandoria.
          • Tillinidae Foissner et al. 2011. Tillina.
        • Grossglockneriidae Foissner 1980 [Grossglockneriina Foissner 1980]. Grossglockneria, Pseudoplatyophrya.
      • Cyrtolophosidida Foissner 1978
        • Cyrtolophosididae Stokes 1888. Cyrtolophosis.
        • Kreyellidae Foissner 1979. Kreyella.
      • Platyophryida de Puytorac et al. 1979
        • Ottowphryidae Foissner et al. 2011. Ottowphrya, Platyophryides.
        • Platyophryidae de Puytorac et al. 1979 (P). Platyophrya.
        • Sagittariidae Grandori & Grandori 1935. Sagittaria.
        • Sorogenidae Bradbury & Olive 1980. Sorogena.
        • Woodruffiidae Gelei 1954. Etoschophrya, Rostrophrya, Woodruffia.
    • Nassophorea (P)
      • Colpodidiidae Foissner 1995. Colpodidium.
      • Nassulida Jankowski 1967
        • Furgasoniidae Corliss 1979. Furgasonia, Wolfkosia.
        • Nassulidae de Fromentel 1874. Nassula, Obertrumia.
      • Microthoracida Jankowski 1967
        • Microthoracidae Wrzesniowski 1870. Drepanomonas, Microthorax.
        • Leptopharyngidae Kahl 1926. Leptopharynx, Pseudomicrothorax.
    • Prostomatea Schewiakoff 1896 (P)
      • Apsiktratidae Foissner et al. 1994 [Prostomatida Schewiakoff 1896]
        • Balanionidae Small & Lynn 1985. Balanion.
        • Cryptocaryonidae Wright & Colorni 2002. Cryptocaryon.
        • Colepidae Ehrenberg 1838. Coleps, Plagiopogon.
        • Holophryidae Perty 1852. Holophrya.
        • Lagynidae Sola et al. 1990. Lagynus.
        • Metacystidae Kahl 1926. Metacystis, Vasicola.
        • Placidae Small & Lynn 1985. Placus.
        • Plagiocampidae Kahl 1926. Plagiocampa.
        • Prorodontidae Kent 1881. Prorodon.
        • Urotrichidae Small & Lynn 1985. Urotricha.
    • Plagiopylea Small & Lynn 1985
      • Plagiopylida Small & Lynn 1985
        • Epalxellidae Corliss 1960. Epalxella, Saprodinium.
        • Plagiopylidae Schewiakoff 1896. Plagiopyla.
        • Sonderiidae Small & Lynn 1985. Sonderia.
        • Trimyemidae Kahl 1933. Trimyema.
    • Oligohymenophorea de Puytorac et al. 1974
      • Apostomatia Chatton & Lwoff 1928
        • Apostomatida Chatton & Lwoff 1928
          • Colliniidae Cépède 1910. Collinia, Metacollinia.
          • Cyrtocaryidae Corliss 1979. Cyrtocaryum.
          • Foettingeriidae Chatton 1911. Foettingeria.
          • Pseudocolliniidae Chantangsi et al. 2013. Fusiforma, Pseudocollinia.
        • Astomatophorida Jankowski 1966
          • Opalinopsidae Hartog 1906. Opalinopsis.
        • Pilisuctorida Jankowski 1966
          • Conidophryidae Kirby 1941. Conidophrys.
      • Astomatia Schewiakoff 1896
        • Anoplophryidae Cépède 1910. Anoplophrya.
        • Buetschliellidae de Puytorac in Corliss 1979. Buetschliella.
        • Clausilocolidae de Puytorac in Corliss 1979. Clausilocola.
        • Contophryidae de Puytorac 1972. Contophyra.
        • Haptophryidae Cépède 1923. Haptophrya.
        • Hoplitophryidae Cheissin 1930. Hoplitophrya.
        • Intoshellinidae Cépède 1910. Intoshellina.
        • Maupasellidae Cépède 1910. Maupasella.
        • Radiophryidae de Puytorac 1972. Radiophrya.
      • Hymenostomatia Delage & Hérouard 1896
        • Tetrahymenida Fauré-Fremiet in Corliss 1956. Incertae sedis taxa: Trichospiridae Kahl 1926 (Trichospira).
          • Curimostomatidae Jankowski 1968. Curimostoma.
          • Glaucomidae Corliss 1971. Glaucoma.
          • Spirozonidae Kahl 1926. Spirozona.
          • Tetrahymenidae Corliss 1952. Tetrahymena.
          • Turaniellidae Didier 1971. Colpidium, Dexiostoma, Turaniella.
        • Ophryoglenida Canella 1964
          • Ichthyophthiriidae Kent 1881. Ichthyophthirius.
          • Ophryoglenidae Kent 1881. Ophryoglena.
      • Peniculia Fauré-Fremiet in Corliss 1956 (P)
        • Peniculida Fauré-Fremiet in Corliss 1956
          • Clathrostomatidae Kahl 1926. Clathrostoma.
          • Frontoniidae Kahl 1926. Disematostoma, Frontonia (P).
          • Lembadionidae Jankowski in Corliss 1979. Lembadion.
          • Maritujidae Jankowski in Small & Lynn 1985. Marituja.
          • Neobursaridiidae Dragesco & Tuffrau 1967. Neobursaridium.
          • Parameciidae Dujardin 1840. Paramecium.
          • Paranassulidae Fauré-Fremiet 1962. Paranassula.
          • Stokesiidae Roque 1961. Stokesia.
        • Urocentridae Claparède & Lachmann 1858 [Urocentrida de Puytorac, Grain & Mignot 1987]
      • Peritrichia Stein 1859
        • Sessilida Kahl 1933
          • Astylozoidae Kahl 1935. Astylozoon, Hastatella.
          • Ellobiophryidae Chatton and Lwoff 1929. Ellobiophrya.
          • Epistylididae Kahl 1933. Epistylis.
          • Lagenophryidae Bütschli 1889. Lagenophrys.
          • Operculariidae Fauré-Fremiet in Corliss 1979. Opercularia.
          • Rovinjellidae Matthes 1972. Rovinjella.
          • Scyphidiidae Kahl 1933 (P). Scyphidia.
          • Termitophryidae Lom in Corliss 1979. Termitophrya.
          • Usconophryidae Clamp 1991. Usconophrys.
          • Vaginicolidae de Fromentel 1874. Cothurnia, Pyxicola, Thuricola, Vaginicola.
          • Vorticellidae Ehrenberg 1838. Carchesium, Epicarchesium (P), Ophrydium, Pelagovorticella, Pseudovorticella (P), Vorticella (P).
          •