- Microcystis aeruginosa (Kützing) Kützing, 1846
- Microcystis botrys Teiling, 1942
- Microcystis flosaquae (Wittrock) Kirchner, 1898
- Microcystis ichthyoblabe (G.Kunze) Kützing, 1843
- Microcystis panniformis Komárek, Komárková-Legnerová, Sant'Anna, M.T.P.Azevedo & P.A.C.Senna, 2002
- Microcystis viridis (A.Braun) Lemmermann, 1903
- Microcystis wesenbergii (Komárek) Komárek ex Komárek, 2006
- Snowella lacustris (Chodat) Komárek & Hindák, 1988