• Microcystis Beck, 1837 [Family: Microcystidae]
• Microcystis F.T. Kützing, 1833 accepted as Euglena Ehrenberg, 1830 [Family: Euglenidae]
• Microcystis Lemmermann, 1907 [Family: Microcystaceae]
• Microcystis aeruginosa (Kützing) Kützing, 1846
• Microcystis aeruginosa phage Ma-LMM01
• Microcystis amethystina (Filarszky) Forti, 1907
• Microcystis anodontae (Hansgirg) Elenkin, 1938 accepted as Aphanocapsa rivularis (Carmicheal) Rabenhorst, 1865
• Microcystis antiqua Odhner, 1917 accepted as Tarocystis antiqua (Odhner, 1917)
• Microcystis aphanothecioides
• Microcystis aphanothecoides Zalessky, 1926 accepted as Aphanothece elabens (Brébisson) Elenkin, 1938
• Microcystis argentea Schiller, 1954
• Microcystis atra Kützing, 1833 accepted as Gloeocapsa atrata Kützing, 1843
• Microcystis bengalensis Banerjii, 1936
• Microcystis botrys Teiling, 1942
• Microcystis bullosa Meneghini, 1837 accepted as Aphanothece bullosa (Meneghini) Rabenhorst, 1865
• Microcystis calciphila Schwabe, 1947 accepted as Aphanocapsa rivularis (Carmicheal) Rabenhorst, 1865
• Microcystis castaneocincta Sykes, 1900 accepted as Greenwoodoconcha castaneocincta (Sykes, 1900)
• Microcystis catletti
• Microcystis chroococcoidea W. West & G.S. West, 1911
• Microcystis clarionensis (Setchell & Gardner) de Toni, 1938
• Microcystis comperei Komárek, 1984
• Microcystis complanata Skuja, 1964
• Microcystis concharum (Hansgirg) P. Silva, 1996
• Microcystis delicatissima (W. West & G.S. West) Starmach, 1966 accepted as Aphanocapsa delicatissima W. West & G.S. West, 1912
• Microcystis densa G.S. West, 1909
• Microcystis densa Schiller, 1956
• Microcystis dimidiata (Kützing) P.C. Silva, 1996
• Microcystis dimorpha Joosten
• Microcystis elabens (Brébisson) Kützing, 1846 accepted as Aphanothece elabens (Brébisson) Elenkin, 1938
• Microcystis elachista (W. West & G.S. West) Compère, 1967
• Microcystis elongata Desikachary, 1959
• Microcystis endophytica (G.M. Smith) Elenkin, 1938
• Microcystis exigua Zalessky, 1926
• Microcystis feldmannii (Frémy) Kosinskaja, 1948 accepted as Aphanocapsa feldmannii Frémy, 1933
• Microcystis ferruginea Wawrik, 1963 accepted as Cyanogranis ferruginea (F. Wawrik) Hindák, 1982
• Microcystis firma (Kützing) Schmidle, 1902
• Microcystis floccosa Zalessky, 1925 accepted as Aphanothece floccosa (Zalessky) G. Cronberg & J. Komárek, 1994
• Microcystis flosaquae (Wittrock) Kirchner, 1898
• Microcystis flos-aquae (Wittrock in Wittrock & Nordstedt) Kirchner, 1898
• Microcystis fonticola (Hansgirg) Kann, 1978 accepted as Aphanocapsa fonticola Hansgirg, 1890
• Microcystis fulva Odhner, 1917 accepted as Tarocystis fulva (Odhner, 1917)
• Microcystis fuscolutea (Hansgirg) Forti, 1907
• Microcystis glauca (Wolle) Drouet & Daily, 1939
• Microcystis grevillei (Berkeley) Elenkin, 1938 accepted as Aphanocapsa grevillei (Hassall) Rabenhorst, 1865
• Microcystis grevillei (Hassall) Elenkin, 1938 accepted as Aphanocapsa grevillei (Hassall) Rabenhorst, 1865
• Microcystis grevillii
• Microcystis halophila B. Martens & Pankow, 1972
• Microcystis hansgirgiana Elenkin, 1938 accepted as
• Microcystis holsatica (Lemmermann) Lemmermann, 1907 accepted as Aphanocapsa holsatica (Lemmermann) G. Cronberg & J. Komárek, 1994
• Microcystis ichthyoblabe Kützing, 1843
• Microcystis ichtyoblable Kützing
• Microcystis icthyoblabe Kützing
• Microcystis incerta (Lemmermann) Lemmermann, 1907 accepted as Aphanocapsa incerta (Lemmermann) Cronberg & Komárek, 1994
• Microcystis inscensa Hedley, 1912 accepted as Dendronitor inscensa (Hedley, 1912)
• Microcystis lamelliformis Holsinger, 1954
• Microcystis leavens (Berthold) Kützing
• Microcystis litoralis (Hansgirg) Forti, 1907 accepted as Aphanocapsa litoralis Hansgirg, 1892
• Microcystis lutescens Schiller, 1954
• Microcystis marginata (Meneghini) Kützing, 1846 accepted as Microcystis novacekii (Komárek) Compère, 1974
• Microcystis marina (Hansgirg) P.C. Silva, 1996
• Microcystis marina Kützing, 1836
• Microcystis maxima Bernard, 1908
• Microcystis merismopedioides Fritsch, 1912
• Microcystis minima Bernard, 1909 accepted as Coelomoron minimum (Bernard) J. Komárková-Legnerová & R. Tavera, 1996
• Microcystis minuta Kylin, 1937
• Microcystis minutissima W. West, 1912 accepted as Aphanothece minutissima (W. West) J. Komárková-Legnerová & G. Cronberg, 1994
• Microcystis montana (Teodorescu) J. De Toni, 1939
• Microcystis montigena Hoffmann, 1986 accepted as Aphanocapsa muscicola (Meneghini) Wille, 1919
• Microcystis muscicola (Meneghini) Elenkin, 1938 accepted as Aphanocapsa muscicola (Meneghini) Wille, 1919
• Microcystis natans Lemmermann ex Skuja, 1934
• Microcystis novacekii (Komárek) Compère, 1974
• Microcystis nux Sykes, 1900 accepted as Greenwoodoconcha nux (Sykes, 1900)
• Microcystis ochracea (Brand) Lemmermann
• Microcystis orae Kosinskaja, 1948 accepted as Aphanocapsa orae (Kosinskaja) Komárek & Anagnostidis, 1995
• Microcystis orissica West, 1911
• Microcystis ovalis Hollenberg, 1939
• Microcystis pallida (Farlow) Lemmermann, 1910
• Microcystis panniformis J. Komárek, J. Komárková-Legnerová, C.L. Sant'Anna, M.T.P. Azevedo & P.A.C. Senna, 2002
• Microcystis parasitica Kützing, 1843 accepted as Aphanocapsa parasitica (Kützing) Komárek & Anagnostidis, 1995
• Microcystis parietina (Nägeli) Elenkin, 1938 accepted as Aphanocapsa parietina Nägeli, 1849
• Microcystis prasina (Wittrock) Lemmermann, 1904 accepted as Microcystis flos-aquae (Wittrock in Wittrock & Nordstedt) Kirchner, 1898
• Microcystis protea Copeland, 1936
• Microcystis protocystis Crow, 1923
• Microcystis protogenita (Biasoletto) Cooke, 1882
• Microcystis pseudofilamentosa Crow, 1923
• Microcystis pulverea (Wood) Forti, 1907
• Microcystis punctata Schiller, 1954 accepted as Microcystis scripta (Richter) Geitler, 1925
• Microcystis ramosa Bharadwaya, 1935
• Microcystis raspaigellae (Hauck) Kosinskaja, 1948 accepted as Aphanocapsa raspaigellae (Hauck) Frémy, 1933
• Microcystis reinboldii (Richter) Forti, 1907
• Microcystis responsivus Hedley, 1912 accepted as Tarocystis responsivus (Hedley, 1912)
• Microcystis richteriana (Hieronymus) P. Silva, 1996
• Microcystis robusta (Clark) Nygaard, 1925
• Microcystis roeseana (De Bary) Elenkin, 1938 accepted as Aphanocapsa roeseana De Bary, 1870
• Microcystis rosea Kufferath, 1942
• Microcystis salina (Woronichin) Elenkin, 1938
• Microcystis salinarum (Hansgirg) P. Silva, 1996
• Microcystis sanguinea (C. Agardh) Kützing, 1833
• Microcystis scripta (Richter) Geitler, 1925
• Microcystis smithii Komárek & Anagnostidis, 1995