• Acanthamoeba castellanii (Douglas, 1930)
• Acanthamoeba gigantea Schmoller, 1964
• Acanthamoeba hatchetti Sawyer, Visvesvara & Harke, 1977
• Acanthamoeba palestinensis (Reich, 1933)
• Acanthamoeba polyphaga (Puschkarew)
• Acanthamoeba rhysodes (Singh, 1953)
• Acanthocorbis apoda (Leadbeater) Hara & Takahashi, 1984
• Acanthocorbis asymmetrica (Thomsen) Hara & Takahashi, 1984
• Acanthocorbis brevipoda accepted as Acanthoeca brevipoda W.Ellis, 1930
• Acanthocorbis camarensis Hara et al., 1996
• Acanthocorbis campanula (Espeland) Thomsen, 1991
• Acanthocorbis haurakiana Thomsen, 1991
• Acanthocorbis nana Thomsen, Garrison & Kosman, 1991
• Acanthocorbis prolongata Thomsen, Garrison & Kosman, 1997
• Acanthocorbis tinnabulum Marchant et al., 1987
• Acanthocorbis tintinnabulum Marchant, van den Hoff & Burton, 1987
• Acanthocorbis unguiculata (Thomsen) Hara & Takahashi, 1984
• Acanthocorbis weddellensis Thomsen, Garrison & Kosman, 1997
• Acanthoeca brevipoda W.Ellis, 1930
• Acanthoeca nana Thomsen, 1997 accepted as Helgoeca nana Leadbeater, 2008
• Acanthoeca spectabilis W.N.Ellis, 1930
• Acanthoecopsis apoda Leadbeater, 1972 accepted as Acanthocorbis apoda (Leadbeater) Hara & Takahashi, 1984
• Acanthoecopsis asymmetrica Thomsen
• Acanthoecopsis campanula Espeland, 1986 accepted as Acanthocorbis campanula (Espeland) Thomsen, 1991
• Acanthoecopsis spiculifera Norris, 1965 accepted as Polyoeca dichotoma W.S.Kent, 1881
• Acanthoecopsis spiculifera R.E.Norris, 1965
• Acanthoecopsis unguiculata Thomsen, 1973 accepted as Acanthocorbis unguiculata (Thomsen) Hara & Takahashi, 1984
• Amoeba agilis Kirk, 1906
• Amoeba biddulphiae
• Amoeba flavescens Gruber, 1889 accepted as Gruberella flavescens (Gruber, 1889) Page, 1984
• Amoeba limax Dujardin, 1841
• Amoeba pulchra Biernacka, 1963 accepted as Thecamoeba pulchra Page, 1977
• Amoenoscapa caudata Hara & Takahashi, 1987
• Amoenoscopa caudata Hara & Takahashi, 1987
• Amphizonella minima Kufferath, 1948
• Ancyromonas abrupta Skvortzov, 1957
• Ancyromonas contorta (Klebs) Lemmermann, 1908
• Ancyromonas lata Skvortzov, 1957 (uncertain)
• Ancyromonas metabolica Skvortzov, 1957 (uncertain)
• Ancyromonas minuta Skvortzov, 1957 (uncertain)
• Ancyromonas nitzschiae Skvortzov, 1957 (uncertain)
• Ancyromonas prima Skvortzov, 1957 (uncertain)
• Ancyromonas rotundata Skvortzov, 1957
• Ancyromonas rugosa Skvortzov, 1957
• Ancyromonas ruminantium Certes, 1889
• Ancyromonas sigmoides Kent, 1881
• Ancyromonas sinistra Al-Qassab, W.J.Lee, Shauna Murray, A.G.B. Simpson & D.J.Patterson, 2002
• Ancyromonas socialis Skvortzov, 1957 (uncertain)
• Antarcella atava Collin, 1914
• Apheloecion antarctica Thomsen, Garrison & Kosman, 1997
• Apheloecion conicoides Thomsen, Garrison & Kosman, 1997
• Apheloecion glacialis Thomsen, Garrison & Kosman, 1997
• Arcella aculeata Ehrenberg, 1832 accepted as Centropyxis aculeata (Ehrenberg, 1832) Stein, 1859
• Arcella brasiliensis A.M.Cunha, 1913 (uncertain)
• Arcella constricta Ehrenberg, 1841 accepted as Centropyxis constricta (Ehrenberg, 1841) Deflandre, 1929
• Arcella dentata Ehrenberg, 1838
• Arcella hemisphaerica Perty, 1852
• Arcella patina Ehrenberg (uncertain)
• Arcella polypora Penard
• Arcella vulgaris Ehrenberg, 1832
• Arcyria denudata (L.) Wettst., 1886
• Arcyria incarnata (Pers. ex J.F. Gmel.) Pers., 1796
• Arundinula capitata (L. Léger & Duboscq) L. Léger & Duboscq, 1906
• Arundinula incurvata (L. Léger & Duboscq) L. Léger & Duboscq, 1906
• Astrosiga disjuncta Kent, 1878
• Aulomonas purdyi Lackey, 1942
• Badhamia macrocarpa (Ces.) Rostaf., 1875
• Bicosta antennigera Moestrup, 1979
• Bicosta minor (Reynolds) Leadbeater, 1978
• Bicosta spinifera (Throndsen) Leadbeater, 1978
• Bullinularia indica (Penard) Deflandre, 1953
• Calliacantha ankyra Thomsen, Garrison & Kosman, 1997
• Calliacantha frigida Thomsen, Garrison & Kosman, 1997
• Calliacantha longicaudata (Leadbeater) Leadbeater, 1978
• Calliacantha multispina Manton & Oates, 1979
• Calliacantha natans (Grøntved) Leadbeater, 1978
• Calliacantha simplex Manton & Oates, 1979
• Calotheca alata Thomsen & Moestrup, 1983
• Campanoeca dilatata Throndsen, 1974 accepted as Polyfibula sphyrelata (Thomsen) Manton, 1981
• Campanoeca pedicellata (Leadbeater, 1972) Throndsen, 1974 accepted as Diaphanoeca pedicellata Leadbeater, 1972
• Campyloacantha spinifera (Leadbeater, 1973) Hara & Takahashi, 1987
• Centropyxiella arenaria Valkanov, 1970
• Centropyxiella elegans Valkanov, 1970
• Centropyxiella gibbula Valkanov, 1970
• Centropyxiella gibbulina Chardez & Thomas, 1980
• Centropyxiella golemanskyi Chardez, 1977
• Centropyxiella lucida Golemansky, 1971
• Centropyxiella oopyxiformis Chardez, 1977
• Centropyxiella platystoma Golemansky, 1981
• Centropyxis aculeata (Ehrenberg, 1832) Stein, 1859
• Centropyxis aculeata var. discoides Penard
• Centropyxis aerophila Deflandre, 1929
• Centropyxis constricta (Ehrenberg, 1841) Deflandre, 1929
• Centropyxis minuta Deflandre, 1929
• Centropyxis platystoma (Penard, 1890) Deflandre, 1929
• Chaos redivivum Linnaeus, 1767 accepted as Panagrellus redivivus (Linnaeus, 1767) Goodey, 1945
• Choanoeca perplexa W.N.Ellis, 1930
• Cladospongia elegans M.O.P.Iyengar & K.R.Ramanathan, 1940
• Clydonella rosenfieldi Sawyer, 1975
• Cochliopodium gallicum Kudryavtsev & Smirnov, 2006