Phylum Cyanobacteria Garcia-Pichel et al. (2020) see Phylum Cyanobacteriota Oren et al. 2022
   Class Cyanophyceae Hauck (1885) see Class Chroococcophyceae Hollerbach et al. 1953
     Order Chroococcales Ardissone (1887) see Order Chroococcales corrig. Ardissone 1887
       Family Microcystaceae Elenkin (1933) see Family Microcystaceae Elenkin 1933
         01 ?Genus Aphanocapsa Nägeli (1849) see Genus Aphanocapsa Nägeli 1849
         02 Genus Aphanothece C. Nägeli (1849), nom. cons. see Genus Aphanothece Nägeli 1849 nom. cons.
         03 ?Genus Asterocapsa H.J. Chu (1952) see Genus Asterocapsa Chu 1952
         04 Genus Chalicogloea M.Roldán, M. Ramírez, J. del Campo, Hern.-Mar. & Komárek (2013) see Genus Chalicogloea Roldán et al. 2013
         05 Genus Coelomoron Buell (1938) see Genus Coelomoron Buell 1938
         06 ?Genus Coelosphaeriopsis Lemmerm. (1899) see Genus Coelosphaeriopsis Lemmermann 1899
         07 ?Genus Coelosphaerium C. Nägeli (1849) see Genus Coelosphaerium Nägeli 1849
         08 Genus Crocosphaera Zehr, Rachel A.Foster, Waterbury & E.Webb (2019) see Genus Crocosphaera Zehr et al. 2019
         09 ?Genus Cyanoaggregatum Werner, Sant'Anna & Azevedo (2008) see Genus Cyanoaggregatum Werner et al. 2008
         10 ?Genus Cyanocatena F. Hindák (1975) see Genus Cyanocatena Hindák 1975
         11 ?Genus Cyanocomperia Hindák (2001) see Genus Cyanocomperia Hindák 2001
         12 ?Genus Cyanogastrum Schiller (1956) see Genus Aphanothece Nägeli 1849 nom. cons.
         13 ?Genus Cyanogranis F. Hindák (1982) see Genus Cyanogranis Hindák 1982
         14 ?Genus Cyanonephron B. Hickel (1985) see Genus Cyanonephron Hickel 1985
         15 ?Genus Cyanostylon L. Geitler (1928) see Genus Cyanostylon Geitler 1928
         16 ?Genus Cyanotetras F. Hindák (1988) see Genus Cyanotetras Hindák 1988
         17 ?Genus Dzensia N.N. Woronichin (1929) see Genus Dzensia Woronichin 1929
         18 ?Genus Eucapsis F.E. Clements & H.L. Shantz (1909) see Genus Eucapsis Clements and Shantz 1909
         19 Genus Gloeothece C. Nägeli (1849), nom. cons. see Genus Gloeothece Nägeli 1849 nom. cons.
         20 ?Genus Hormothece C.C. Jao (1944) see Genus Hormothece Jao 1944
         21 ?Genus Mantellum P.J.L.Dang. (1949) see Genus Mantellum Dangeard 1949
         22 Genus Merismopedia F.J.F. Meyen (1839) see Genus Merismopedia Meyen 1839
         23 Genus Microcystis Lemmerm. (1907), nom. cons. see Genus Microcystis Kützing ex Lemmermann 1907 nom. cons.
         24 ?Genus Pannus B. Hickel (1991) see Genus Pannus Hickel 1991
         25 ?Genus Planctocyanocapsa orth. inval. see Genus Planktocyanocapsa Hindák (2002)
         26 ?Genus Pseudoncobyrsa Geitler (1925) see Genus Pseudoncobyrsa Geitler 1925
         27 ?Genus Radiocystis H. Skuja (1948) see Genus Radiocystis Skuja 1948
         28 Genus Rippkaea Johansen & Mareš (2019) see Genus Rippkaea Johansen and Mareš 2019
         29 ?Genus Siphonosphaera Hindák (1988) see Genus Siphonosphaera Hindák 1988
         30 Genus Snowella A.A. Elenkin (1938) see Genus Snowella Elenkin 1938
         31 Genus Sphaerocavum Azevedo & Sant'Anna (2003) see Genus Sphaerocavum Azevedo and Sant'Anna 2003
         32 Genus Synechocystis C. Sauvageau (1893) see Genus Synechocystis Sauvageau 1893
         33 Genus Woronichinia A.A. Elenkin (1933) see Genus Woronichinia Elenkin 1933
         34 Genus Zehria Johansen & Mareš (2019) see Genus Zehria Johansen and Mareš 2019