• Acanthamoeba astronyxis (Ray & Hayes, 1954)
• Acanthamoeba castellanii (Douglas, 1930)
• Acanthamoeba comandoni Pussard, 1964
• Acanthamoeba culbertsoni (Singh & Das, 1970)
• Acanthamoeba gigantea Schmoller, 1964
• Acanthamoeba griffini Sawyer, 1971
• Acanthamoeba hatchetti Sawyer, Visvesvara & Harke, 1977
• Acanthamoeba hyalina (Dobell & O'Connor, 1921)
• Acanthamoeba lenticulata Molet & Ermolieff-Braun, 1976
• Acanthamoeba palestinensis (Reich, 1933)
• Acanthamoeba polyphaga (Puschkarew, 1913)
• Acanthamoeba rhysodes (Singh, 1953)
• Acanthamoeba royreba Willaert, Stevens & Tyndall, 1978
• Acanthamoeba stevensoni Sawyer, Nerad, Lewis & McLaughlin, 1993
• Acanthamoeba terricola Pussard, 1964
• Acanthamoeba tubiashi Lewis & Sawyer, 1979
• 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. Ellis, 1930
• Acanthoecopsis apoda Leadbeater, 1972 accepted as Acanthocorbis apoda (Leadbeater) Hara & Takahashi, 1984
• Acanthoecopsis asymmetrica Thomsen accepted as Acanthocorbis asymmetrica (Thomsen) Hara & Takahashi, 1984
• Acanthoecopsis campanula Espeland, 1986 accepted as Acanthocorbis campanula (Espeland) Thomsen, 1991
• Acanthoecopsis spiculifera Norris, 1965 accepted as Polyoeca dichotoma (Kent)
• Acanthoecopsis unguiculata Thomsen, 1973 accepted as Acanthocorbis unguiculata (Thomsen) Hara & Takahashi, 1984
• Adelphamoeba galeacystis J. Napolitano, M. Wall & C. Ganz
• Aethalium candidum (Pers.) Schltdl., 1827 accepted as Fuligo candida Pers., 1796
• Aethalium flavum (Pers.) Link, 1816 accepted as Fuligo septica (L.) F.H. Wigg., 1780
• Aethalium muscorum (Alb. & Schwein.) Schwein., 1832 accepted as Fuligo muscorum Alb. & Schwein., 1805
• Aethalium rufum (Pers.) Wallr., 1833 accepted as Fuligo rufa Pers., 1794
• Aethalium septicum (L.) Fr., 1829 accepted as Fuligo septica (L.) F.H. Wigg., 1780
• Alacrinella limnoriae Manier & Ormières ex Manier, 1968
• Alacrinella sanjuanensis Hibbits, 1979
• Amastigomonas borokiensis Hamar
• Amastigomonas caudata Mylnikov, 1989
• Amastigomonas debruynei De Saeleer
• Amastigomonas mutabilis (Griessmann) Molina & Nerad
• Amaurochaete atra (Alb. & Schwein.) Rostaf., 1873
• Amaurochaete cribrosa (Fr.) T. Macbr., 1917 accepted as Amaurochaete tubulina (Alb. & Schwein.) T. Macbr., 1922
• Amaurochaete fuliginosa T. Macbr., 1899 accepted as Amaurochaete atra (Alb. & Schwein.) Rostaf., 1873
• Amaurochaete trechispora T. Macbr. & G.W. Martin, 1932
• Amaurochaete tubulina (Alb. & Schwein.) T. Macbr., 1922
• Amiba limax Dujardin
• Amoeba biddulphiae
• Amoeba chaetognathi Grassi
• Amoeba chlorochlamys R. Lauterborn
• Amoeba discoides Sch.
• Amoeba dubia Sch.
• Amoeba flavescens Gruber, 1889 accepted as Gruberella flavescens (Gruber, 1889) Page, 1984
• Amoeba gorgonia Penard, 1902
• Amoeba guttula Duj.
• Amoeba limicola Rhumb.
• Amoeba pigmentifera Grassi
• Amoeba proteus (Pal.)
• Amoeba pulchra Biernacka, 1963 accepted as Thecamoeba pulchra Page, 1977
• Amoeba punctata P.-A. Dangeard
• Amoeba radiosa Ehr.
• Amoeba rotatoria A.F. Mayer
• Amoeba spumosa Grub.
• Amoeba striata Pen.
• Amoeba verrocosa
• Amoeba vespertilio Pen.
• Amoebidium australiense Lichtw. & M.C. Williams, 1992
• Amoebidium colluviei Lichtw., 1998
• Amoebidium fasciculatum J.L. Licht., 1917 accepted as Amoebidium parasiticum Cienkowski, 1861
• Amoebidium parasiticum Cienkowski, 1861
• Amoebidium poissonii Duboscq, L. Léger & Tuzet, 1948 accepted as Amoebidium parasiticum Cienkowski, 1861
• Amoebidium recticola Chatton, 1906
• Amoenoscopa caudata Hara & Takahashi, 1987
• Amphizonella minima Kufferath
• Ancyromonas abrupta Skvortzov
• Ancyromonas contorta (Klebs) Lemmermann
• Ancyromonas lata Skvortzov
• Ancyromonas metabolica Skvortzov
• Ancyromonas minuta Skvortzov
• Ancyromonas nitzschiae Skvortzov
• Ancyromonas parasitica Massart
• Ancyromonas prima Skvortzov
• Ancyromonas rotundata Skvortzov
• Ancyromonas rugosa Skvortzov
• Ancyromonas ruminantium Certes, 1889 accepted as Selenomonas ruminantium (Certes, 1889) Wenyon, 1926
• Ancyromonas sigmoides W.S. Kent
• Ancyromonas socialis Skvortzov
• Antarcella atava Collin, 1914
• Antonigeppia conica (Pers.) Kuntze, 1898 accepted as Lycogala conicum Pers., 1801
• 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