• Amphidinium Claparède & Lachmann, 1859
• Amphidinium achromaticum Skvortzov, 1958
• Amphidinium aculeatum Daday
• Amphidinium aculeatum Schröder
• Amphidinium acutissimum Schiller, 1933
• Amphidinium acutum Lohmann
• Amphidinium ae Kofoid & Swezy
• Amphidinium aeschrum T.M. Harris, 1941
• Amphidinium alinii Skvortzov, 1958
• Amphidinium aloxalocium Norris, 1961
• Amphidinium amphidinioides (Geitler) Schiller, 1932
• Amphidinium amygdalus Cleve-Euler
• Amphidinium asymmetricum Kofoid & Swezy, 1921
• Amphidinium aureum Bohm, 1976
• Amphidinium belauense R.K. Trench, 1993
• Amphidinium bidentatum Schiller, 1955
• Amphidinium bipes Herdman, 1924
• Amphidinium boekhoutensis Caljon, 1983
• Amphidinium boekhoutnesis Caljon, 1983 accepted as Amphidinium incoloratum Campbell, 1973
• Amphidinium boggayum Shauna Murray & D.J. Patterson, 2002
• Amphidinium bourrellyi Wawrik, 1982 accepted as Amphidinium amphidinioides (Geitler) Schiller, 1932
• Amphidinium britannicum (Herdman) Lebour, 1925
• Amphidinium bulbosum Cleve-Euler
• Amphidinium caerulescens Schiller, 1955
• Amphidinium carbunculus Conrad & Kufferath, 1954
• Amphidinium carota Cleve-Euler
• Amphidinium carterae Hulburt, 1957
• Amphidinium celastinum Conrad & Kufferath
• Amphidinium celestinum Conrad & Kufferath, 1954
• Amphidinium chattonii (Hovasse) D.L. Taylor, 1971 accepted as Endodinium chattonii Hovasse, 1922
• Amphidinium coeruleum Conrad, 1939
• Amphidinium coeruluem Conrad
• Amphidinium compressum (Calkins) Taylor & Baillie, 1974
• Amphidinium conradii J. Schiller
• Amphidinium conus Schiller, 1933
• Amphidinium coprosum Baumeister, 1943
• Amphidinium corallinum Conrad & Kufferath
• Amphidinium corpulentum Kofoid & Swezy, 1921
• Amphidinium corrugatum Larsen & D.J. Patterson, 1990
• Amphidinium crassum Lohmann, 1908
• Amphidinium cristatum Ballantine, 1964
• Amphidinium cryophilum G.J. Wedemayer, L.W. Wilcox & L.E. Graham, 1982
• Amphidinium cucurbita Kofoid & Swezy, 1921
• Amphidinium cucurbitella Kofoid & Swezy, 1921
• Amphidinium cupulatisquama M. Tamura & T. Horiguchi
• Amphidinium curvatum Schiller, 1928
• Amphidinium cyaneoturbo Conrad & Kufferath, 1954
• Amphidinium dentatum Kofoid & Swezy, 1921
• Amphidinium diploconus Cleve-Euler
• Amphidinium discoidale (Diesing) Kofoid & Swezy, 1921
• Amphidinium discoidalis (Diesing) Kofoid & Swezy
• Amphidinium dubium Conrad & Kufferath
• Amphidinium eilatiensis J.J. Lee
• Amphidinium elegans Grell & Wohlfarth-Bottermann, 1957
• Amphidinium elenkinii Skvortzov, 1925
• Amphidinium elongatum Cleve-Euler
• Amphidinium eludens E.C. Herdman, 1922 accepted as Adenoides eludens (E.C. Herdman) E. Balech, 1956
• Amphidinium eludens Lebour, 1925 accepted as Adenoides eludens (E.C. Herdman) E. Balech, 1956
• Amphidinium eludens Schiller, 1933 accepted as Adenoides eludens (E.C. Herdman) E. Balech, 1956
• Amphidinium emarginatum (Dies) Kofoid & Swezy
• Amphidinium emarginaum (Deising) Kofoid & Swezy, 1921
• Amphidinium eucephalum Schiller, 1955 accepted as Prosoaulax lacustris (F. Stein) Calado & Moestrup, 2005
• Amphidinium extensum Wulff, 1916
• Amphidinium fastigium Kofoid & Swezy, 1921
• Amphidinium filum Bohm, 1976
• Amphidinium flagellans Schiller
• Amphidinium flexum Herdman, 1923
• Amphidinium fusiforme G.W. Martin
• Amphidinium galbanum Kofoid & Swezy, 1921
• Amphidinium geitleri Huber-Pestalozzi, 1950 accepted as Amphidinium amphidinioides (Geitler) Schiller, 1932
• Amphidinium gibbosum (L. Maranda & Y. Shimizu) Flø Jørgensen & Shauna Murray, 2004
• Amphidinium glabrum M. Hoppenrath & Y.B. Okolodkov, 2000
• Amphidinium glaucovirescens Schiller, 1955
• Amphidinium glaucum W. Conrad, 1926
• Amphidinium globosum Schröder, 1911
• Amphidinium gyrinum T.M. Harris, 1940 accepted as Amphidinium elenkinii Skvortzov, 1925
• Amphidinium hadai Balech, 1976
• Amphidinium herdmanii Kofoid & Swezy, 1921
• Amphidinium hoefleri Schiller & Diskus
• Amphidinium hofleri Schiller & Diskus, 1955 accepted as Amphidinium operculatum Claparède & Lachmann, 1859
• Amphidinium hyalinum Entz, 1930 accepted as Amphidinium elenkinii Skvortzov, 1925
• Amphidinium incoloratum Campbell, 1973
• Amphidinium inconstans Schiller, 1955 accepted as Prosoaulax lacustris (F. Stein) Calado & Moestrup, 2005
• Amphidinium inflatum Kofoid, 1931
• Amphidinium kesselitzii Schiller
• Amphidinium kesslitzii Schiller, 1928
• Amphidinium klebsii Carter, 1937 accepted as Amphidinium carterae Hulburt, 1957
• Amphidinium klebsii Kofoid & Swezy, 1921 accepted as Amphidinium operculatum Claparède & Lachmann, 1859
• Amphidinium kofoidi Lebour, 1925 accepted as Adenoides kofoidii (Herdman) Dodge, 1982
• Amphidinium kofoidi Schiller, 1933 accepted as Adenoides kofoidii (Herdman) Dodge, 1982
• Amphidinium kofoidii E.C. Herdman, 1922 accepted as Adenoides kofoidii (Herdman) Dodge, 1982
• Amphidinium lacunarum Skuja, 1964
• Amphidinium lacustre F. Stein, 1883
• Amphidinium lacustriforme Schiller, 1928 accepted as Amphidinium lacustre F. Stein, 1883
• Amphidinium lanceolatum Schröder, 1911
• Amphidinium larvale Lindemann, 1928 accepted as Amphidinium elenkinii Skvortzov, 1925
• Amphidinium latum Lebour, 1925
• Amphidinium lefevrei Skvortzov, 1968
• Amphidinium lilloense Conrad & Kufferath
• Amphidinium lissae Schiller, 1925