1. Phylum [Unassigned]
   1. Class Ebriophyceae
   2. Class [Unassigned]
      1. Order [Unassigned]
         1. Family [Unassigned]
            1. Genus Acomia
            2. Genus Actipilion Loeblich Jr.
            3. Genus Alisum Górka
            4. Genus Bosporella Hovasse
            5. Genus Centrasphaeridium R.Wicander & G.Playford, 1985
            6. Genus Cephalotrichum
            7. Genus Clautriavia Massart, 1900
            8. Genus Cruzella Faria, A.M.Cunha & C.Pinto
            9. Genus Cymatiogalea J.Deunff, 1961
            10. Genus Daphnidium Cienkowski
            11. Genus Diexallophasis A.R.Loeblich, 1970
            12. Genus Dinomonas W.S.Kent, 1881
            13. Genus Fusopsis A. Meunier, 1910
            14. Genus Halodinium J.P.Bujak, 1984
            15. Genus Kiitoksia Vors, 1992
            16. Genus Meteora
            17. Genus Notoselenus
            18. Genus Oodinioides Reichenbach-Klinke, 1970
            19. Genus Pacillina Cleve, 1899
            20. Genus Pirsonia Schnepf, Drebes & Elbrächter, 1990
            21. Genus Poropila J.Schiller, 1925
            22. Genus Rigidomastix Alexeieff, 1929
            23. Genus Subrhynchopus Skvortsov & Noda, 1983
            24. Genus Subulatomonas L.Katz, J.Grant, L.W.Parfrey, A.Gant, C.O'Kelly, O.R.Anderson, R.E.Molestina & T.Nerad, 2011
            25. Genus Tetracilia
            26. Genus Tetradimorpha T.S.Hsiung, 1927
            27. Genus Trochisciaopsis H.Kufferath
            28. Genus Urceolopsis A.C.Stokes
            29. Genus Vitrella Oborník et al., 2012
            30. Genus Wilsonastrum Jansonius
            31. Genus Helcomastix G.A.Senn, 1911 (uncertain > nomen dubium)

1. Phylum Acritarcha
2. Phylum Amoebozoa
3. Phylum Apusozoa
4. Phylum Choanozoa
5. Phylum Euglenozoa
6. Phylum Hemimastigophora
7. Phylum Loukozoa
8. Phylum Metamonada
9. Phylum Percolozoa
10. Phylum Sulcozoa
11. Phylum Choanoflagellata accepted as Choanozoa (synonym)
12. Phylum Chrysomonada accepted as Heterokontophyta
13. Phylum Dinomastigota accepted as Dinophyta accepted as Dinophyceae
14. Phylum Dinophyta accepted as Dinophyceae
15. Phylum Discomitochondria (disused)
16. Phylum Flagellates accepted as Protozoa (abandoned as taxonomic group)
17. Phylum Granuloreticulosa (disused)
18. Phylum Haptomonada accepted as Haptophyta
19. Phylum Labyrinthulata accepted as Bigyra
20. Phylum Myxospora accepted as Myxozoa
21. Phylum Phaeophycota accepted as Phaeophyceae (synonym)
22. Phylum Phaeophyta accepted as Phaeophyceae
23. Phylum Rhizopoda (disused)
24. Phylum Sarcomastigophora (disused)
25. Phylum Apusomonada (uncertain > unassessed)

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