• Anacystis dimidiata (Kützing) Drouet & Daily, 1952 accepted as Chroococcus turgidus (Kützing) Nägeli, 1849
• Anacystis marina (Hansgirg) Drouet & Daily, 1948 accepted as Aphanocapsa marina Hansgirg, 1890
• Gloeocapsa aeruginosa Kützing, 1843
• Gloeocapsa arenaria (Hassall) Rabenhorst, 1865
• Gloeocapsa atrata Kützing, 1843
• Gloeocapsa biformis Ercegovic, 1925
• Gloeocapsa bituminosa (Bory de Saint-Vincent) Kützing, 1849
• Gloeocapsa caldariorum Rabenhorst, 1865
• Gloeocapsa compacta Kützing, 1847
• Gloeocapsa crepidinum (Thuret) Thuret, 1876 accepted as Gloeocapsopsis crepidinum (Thuret) Geitler ex Komárek, 1993
• Gloeocapsa decorticans (A.Braun) P.Richter, 1925
• Gloeocapsa gelatinosa Kützing, 1843
• Gloeocapsa kuetzingiana Nägeli ex Kützing, 1849
• Gloeocapsa punctata Nägeli, 1849
• Gloeocapsa rupestris Kützing, 1847
• Gloeocapsa sanguinea (C.Agardh) Kützing, 1843
• Gloeocapsa thermalis Lemmermann, 1905 (uncertain)
• Gloeocapsa thermophila (Wood) Claus, 1959
• Microcystis aeruginosa (Kützing) Kützing, 1846
• Microcystis aeruginosa f. flos-aquae (Wittrock) Elenkin, 1938 accepted as Microcystis flosaquae (Wittrock) Kirchner, 1898
• Microcystis aeruginosa f. viridis (A.Braun) Elenkin, 1938 accepted as Microcystis viridis (A.Braun) Lemmermann, 1903
• Microcystis firma (Kützing) Schmidle, 1902
• Microcystis flosaquae (Wittrock) Kirchner, 1898
• Microcystis flos-aquae (Wittrock in Wittrock & Nordstedt) Kirchner, 1898
• Microcystis grevillei (Berkeley) Elenkin, 1938 accepted as Aphanocapsa grevillei (Berkeley) Rabenhorst, 1865
• Microcystis grevillei f. pulchra (Kützing) Elenkin, 1936 accepted as Microcystis smithii Komárek & Anagnostidis, 1995
• Microcystis holsatica (Lemmermann) Lemmermann, 1907 accepted as Aphanocapsa holsatica (Lemmermann) G.Cronberg & Komárek, 1994
• Microcystis ichthyoblabe (G.Kunze) Kützing, 1843
• Microcystis incerta (Lemmermann) Lemmermann, 1903 accepted as Aphanocapsa incerta (Lemmermann) G.Cronberg & Komárek, 1994
• Microcystis marginata (Meneghini) Kützing, 1846
• Microcystis novacekii (Komárek) Compère, 1974
• Microcystis panniformis Komárek, Komárková-Legnerová, Sant'Anna, M.T.P.Azevedo & P.A.C.Senna, 2002
• Microcystis pulverea (H.C.Wood) Forti, 1907
• Microcystis scripta (P.Richter) Lemmermann, 1903
• Microcystis smithii Komárek & Anagnostidis, 1995
• Microcystis stagnalis (Lemmermann) Lemmermann, 1903 accepted as Aphanocapsa stagnalis (Lemmermann) Belyakova, 2004
• Microcystis viridis (A.Braun) Lemmermann, 1903
• Microcystis wesenbergii (Komárek) Komárek ex Komárek, 2006
• Polycystis elabens (Brébisson) Kützing, 1849 accepted as Aphanothece elabens (Meneghini) Elenkin, 1936
• Polycystis elabens var. ichthyoblabe (Kützing) Hansgirg accepted as Microcystis ichthyoblabe (G.Kunze) Kützing, 1843
• Radiocystis geminata Skuja, 1948
• Sphaerocavum microcystiforme (Hindák) Azevedo & Sant' Anna, 2003