• Anacystis aeruginosa (Zanardini) Drouet & Daily, 1948 accepted as Microcystis zanardinii (Hauck) P. Silva, 1996
• Anacystis amplivesiculata Gardner, 1927
• Anacystis anaptis B. Biswal
• Anacystis anomala Gardner, 1927
• Anacystis botryoides (Linnaeus) Meneghini
• Anacystis brunnea (A. Braun) Wolle
• Anacystis compacta Gardner, 1927
• Anacystis consociata Gardner
• Anacystis cyanea (Kützing) F.E. Drouet & W.A. Daily, 1952
• Anacystis cylindracea Gardner
• Anacystis dimidiata (Kützing) Drouet & Daily, 1952 accepted as Chroococcus dimidiatus (Kützing) Nägeli, 1849
• Anacystis distans Gardner
• Anacystis elabens (Brébisson) Setchell & Gardner, 1918 accepted as Aphanothece elabens (Brébisson) Elenkin, 1938
• Anacystis firma (Kützing) Drouet & Daily
• Anacystis furfuracea (Berkeley) Meneghini
• Anacystis gigas (W. West & G.S. West) Gardner
• Anacystis glauca Wolle, 1877 accepted as Microcystis glauca (Wolle) Drouet & Daily, 1939
• Anacystis gloeocapsoides Gardner, 1927
• Anacystis grevillei (M.J. Berkeley) Kützing
• Anacystis hyalina Chu
• Anacystis incerta (Lemmermann) F.E. Drouet & W.A. Daily, 1952 accepted as Aphanocapsa incerta (Lemmermann) Cronberg & Komárek, 1994
• Anacystis irregularis Gardner
• Anacystis limnetica (Lemmermann) Drouet & Daily, 1952 accepted as Chroococcus limneticus Lemmermann, 1898
• Anacystis magnifica Gardner, 1927 accepted as Asterocapsa magnifica (Gardner) J. Komárek, 1993
• Anacystis marginata Meneghini
• Anacystis marina (Hansgirg) Drouet & Dailey, 1948 accepted as Microcystis marina (Hansgirg) P.C. Silva, 1996
• Anacystis microsphaeria Gardner, 1927
• Anacystis minuta (C. Agardh) Meneghini
• Anacystis minutissima Gardner, 1927
• Anacystis montana (Lightfoot) Drouet & Daily, 1952 accepted as Gloeocapsa atrata Kützing, 1843
• Anacystis nidulans (Richt.) Drouet & Daily
• Anacystis nidulans Gardner
• Anacystis nigropurpurea Gardner
• Anacystis nigroviolacea Gardner
• Anacystis paludosa Rabenhorst
• Anacystis parasitica (Kützing) Trevisan, 1848 accepted as Aphanocapsa parasitica (Kützing) Komárek & Anagnostidis, 1995
• Anacystis peniocystis (Kützing) Drouet & Daily
• Anacystis pulchra Gardner, 1927 accepted as Asterocapsa pulchra (Gardner) J. Komárek, 1993
• Anacystis pulvereus (Wood) Wolle
• Anacystis purpurea C.C. Jao
• Anacystis radiata Gardner
• Anacystis reinboldii Richter, 1891 accepted as Microcystis reinboldii (Richter) Forti, 1907
• Anacystis rupestris (Lyngbye) Drouet & Daily
• Anacystis thermalis (Meneghini) Drouet & Daily, 1952
• Anacystis trochiscioides C.C. Jao
• Anacystis willei Gardner
• Cagniardia adriatica (Kützing) Trevisan, 1848 accepted as Aphanocapsa le-jolisii (Thuret) Frémy, 1924
• Cagniardia cyanea (Kützing) Trevisan accepted as Anacystis cyanea (Kützing) F.E. Drouet & W.A. Daily, 1952
• Clathrocystis aeruginosa (Kützing) Henfrey, 1856 accepted as Microcystis aeruginosa (Kützing) Kützing, 1846
• Clathrocystis holsatica Lemmermann, 1903 accepted as Aphanocapsa holsatica (Lemmermann) G. Cronberg & J. Komárek, 1994
• Clathrocystis montana Teodorescu, 1907 accepted as Microcystis montana (Teodorescu) J. De Toni, 1939
• Clathrocystis roseo-persicina (Kützing, 1849) Cohn, 1875 accepted as Lamprocystis roseopersicina (Kützing 1849) Schröter, 1886
• Cyanocomperia africana Hindák, 2002
• Diplocystis elabens (Brébisson) Trevisan, 1848 accepted as Aphanothece elabens (Brébisson) Elenkin, 1938
• Diplocystis ichthyoblabe (G. Kunze) Trevisan, 1848 accepted as Microcystis ichthyoblabe Kützing, 1843
• Diplocystis incerta (Lemmermann) F.E. Drouet & W.A. Daily
• Diplocystis pulverea (H.C. Wood) R. Margalef, 1952 accepted as Microcystis pulverea (Wood) Forti, 1907
• Micraloa aeruginosa Kützing, 1833 accepted as Microcystis aeruginosa (Kützing) Kützing, 1846
• Micraloa aurantiaca (Kützing) Trevisan
• Micraloa botryoides (Kützing) Trevisan
• Micraloa elabens Brébisson, 1842 accepted as Aphanothece elabens (Brébisson) Elenkin, 1938
• Micraloa firma (Kützing) Trevisan
• Micraloa flosaquae (Linnaeus) Trevisan, 1845 accepted as Aphanizomenon flosaquae Ralfs ex Bornet & Flahault, 1886
• Micraloa glomerata (Brébisson) Meneghini
• Micraloa olivacea Kützing
• Micraloa pallida (Kützing) Trevisan
• Micraloa pini (Kützing) Trevisan
• Micraloa pini-turinorum Biasoletto, 1832
• Micraloa protogenita Biasoletto, 1832
• Micraloa rosea Kützing, 1833 accepted as Lamprocystis roseopersicina (Kützing 1849) Schröter, 1886
• Micraloa rupestris (Lyngbye) Trevisan
• Micraloa teres Flotow
• Microcystis aeruginosa (Kützing) Kützing, 1846
• Microcystis amethystina (Filarszky) Forti, 1907
• Microcystis anodontae (Hansgirg) Elenkin, 1938 accepted as Aphanocapsa rivularis (Carmicheal) Rabenhorst, 1865
• 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 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