• 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
• Anacystis montana (Lightfoot) Drouet & Daily, 1952 accepted as Gloeocapsa atrata Kützing, 1843
• Aphanocapsa delicatissima West & G.S.West, 1912
• Aphanocapsa elachista West & G.S.West, 1894
• Aphanocapsa elachista var. irregularis J.B.Petersen, 1923 accepted as Microcystis pulverea f. irregularis (J.B.Petersen) Elenkin
• Aphanocapsa endolithica Ercegović, 1925 accepted as Aphanocapsa rivularis (Carmichael) Rabenhorst, 1865
• Aphanocapsa grevillei (Berkeley) Rabenhorst, 1865
• Aphanocapsa marina Hansgirg, 1890
• Aphanocapsa montana C.E.Cramer, 1862 accepted as Aphanocapsa muscicola (Meneghini) Wille, 1919
• Aphanocapsa muscicola (Meneghini) Wille, 1919
• Aphanocapsa parasitica (Kützing) Komárek & Anagnostidis, 1995
• Aphanocapsa parietina Nägeli, 1849
• Aphanocapsa rivularis (Carmichael) Rabenhorst, 1865
• Aphanocapsa stagnalis (Lemmermann) Beljakova, 2004
• Aphanothece castagnei (Kützing) Rabenhorst, 1865
• Aphanothece clathrata West & G.S.West, 1906 accepted as Anathece clathrata (West & G.S.West) Komárek, Kastovsky & Jezberová, 2011
• Aphanothece elabens (Meneghini) Elenkin, 1936
• Aphanothece nidulans P.Richter, 1884
• Aphanothece pallida (Kützing) Rabenhorst, 1863
• Aphanothece prasina A.Braun, 1863 accepted as Aphanothece stagnina (Sprengel) A.Braun, 1863
• Aphanothece saxicola Nägeli, 1849
• Aphanothece stagnina (Sprengel) A.Braun, 1863
• Chondrocystis dermochroa (Nägeli) Komárek & Anagnostidis, 1995
• Chroococcus cohaerens (Brébisson) Nägeli, 1849
• Chroococcus cohaerens var. antarcticus Wille, 1924 (uncertain)
• Chroococcus dispersus (Keissler) Lemmermann, 1904
• Chroococcus giganteus West, 1892
• Chroococcus helveticus Nägeli, 1849
• Chroococcus limneticus Lemmermann, 1898 accepted as Limnococcus limneticus (Lemmermann) Komárková, Jezberová, O.Komárek & Zapomelová, 2010
• Chroococcus minor (Kützing) Nägeli, 1849
• Chroococcus minor var. dispersus Keissler, 1902 accepted as Chroococcus dispersus (Keissler) Lemmermann, 1904
• Chroococcus minutus (Kützing) Nägeli, 1849
• Chroococcus minutus f. obliteratus (Richter) Hansgirg accepted as Chroococcus obliteratus Richter, 1885
• Chroococcus montanus Hansgirg, 1891
• Chroococcus obliteratus Richter, 1885
• Chroococcus pallidus Nägeli, 1849
• Chroococcus turgidus (Kützing) Nägeli, 1849
• Chroococcus westii J.B.Petersen, 1923
• Coccochloris aeruginosa (Nägeli) F.E.Drouet & W.A.Daily, 1952 accepted as Cyanothece aeruginosa (Nägeli) Komárek, 1976
• Coccochloris stagnina Sprengel, 1807 accepted as Aphanothece stagnina (Sprengel) A.Braun, 1863
• Coelosphaerium dubium Grunow, 1865
• Cyanobacterium cedrorum (Sauvageau) Komárek, J.Kopecký & Cepák, 1999
• Cyanosarcina chroococcoides (Geitler) Kovácik, 1988
• Cyanosarcina spectabilis (Geitler) Kovácik, 1988
• Dactylococcopsis antarctica F.E.Fritsch, 1912
• Dactylococcopsis irregularis G.M.Smith, 1922 accepted as Monoraphidium irregulare (G.M.Smith) Komárková-Legnerová, 1969
• Dactylococcopsis rhaphidioides Hansgirg, 1888
• Dactylococcopsis smithii R.Chodat & F.Chodat, 1925 accepted as Rhabdogloea smithii (R.Chodat & F.Chodat) Komárek, 1983
• Eucapsis alpina F.E.Clements & H.L.Schantz, 1909
• Eucapsis minor (Skuja) Elenkin, 1933
• Eucapsis minuta F.E.Fritsch, 1912
• Gloeothece palea (Kützing) Nägeli, 1849
• Gloeothece rupestris (Lyngbye) Bornet, 1880
• Johanseninema constrictum (Szafer) Hasler, Dvorák & Poulícková, 2014
• Limnococcus limneticus (Lemmermann) Komárková, Jezberová, O.Komárek & Zapomelová, 2010
• Merismopedia punctata Meyen, 1839 accepted as Merismopedia tranquilla (Ehrenberg) Trevisan, 1845
• Merismopedia tenuissima Lemmermann, 1898
• Merismopedia tranquilla (Ehrenberg) Trevisan, 1845
• Merismopedia warmingiana (Lagerheim) Forti, 1907
• Microcystis aeruginosa (Kützing) Kützing, 1846
• Microcystis elabens (Brébisson) Kützing, 1846 accepted as Aphanothece elabens (Meneghini) Elenkin, 1936
• Microcystis elachista (West & G.S.West) Starmach, 1966 accepted as Aphanocapsa elachista West & G.S.West, 1894
• Microcystis fuscolutea (Hansgirg) Forti, 1907
• Microcystis grevillei (Berkeley) Elenkin, 1938 accepted as Aphanocapsa grevillei (Berkeley) Rabenhorst, 1865
• Microcystis marginata (Meneghini) Kützing, 1846
• Microcystis merismopedioides F.E.Fritsch, 1912
• Microcystis muscicola (Meneghini) Elenkin, 1938 accepted as Aphanocapsa muscicola (Meneghini) Wille, 1919
• Microcystis novacekii (Komárek) Compère, 1974
• Microcystis parasitica Kützing, 1843 accepted as Aphanocapsa parasitica (Kützing) Komárek & Anagnostidis, 1995
• Microcystis parietina (Nägeli) Elenkin, 1938 accepted as Aphanocapsa parietina Nägeli, 1849
• Microcystis pulverea (H.C.Wood) Forti, 1907
• Microcystis pulverea f. irregularis (J.B.Petersen) Elenkin
• Microcystis stagnalis (Lemmermann) Lemmermann, 1903 accepted as Aphanocapsa stagnalis (Lemmermann) Beljakova, 2004
• Microcystis wesenbergii (Komárek) Komárek ex Komárek, 2006
• Myxosarcina chroococcoides Geitler, 1927 accepted as Cyanosarcina chroococcoides (Geitler) Kovácik, 1988
• Myxosarcina concinna Printz, 1921
• Myxosarcina spectabilis Geitler, 1933 accepted as Cyanosarcina spectabilis (Geitler) Kovácik, 1988
• Pleurocapsa minor Hansgirg, 1891
• Pleurocapsa polonica Raciborski, 1910 accepted as Siphononema polonicum (Raciborski) Geitler, 1925
• Siphononema polonicum (Raciborski) Geitler, 1925
• Siphononema polonicum Geitler, 1931 (uncertain)
• Synechocystis aquatilis Sauvageau, 1892
• Synechocystis crassa Woronichin, 1929
• Synechocystis minuscula Woronichin, 1926
• Synechocystis pevalekii Ercegović, 1925
• Synechocystis sallensis Skuja, 1930
• Xenococcus schousboei Thuret, 1880