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
       1.1.1 Family Microcystaceae Elenkin (1933) see Family Microcystaceae Elenkin 1933
       1.1.2.1 Family Geminocystaceae Tuji, Yamaguchi & Niiyama (2021) see Family Geminocystaceae Tuji et al. 2021
       1.1.2.2 Family Cyanotrichaceae Elenkin (1947), nom. illeg. see Family Chroococcaceae Nägeli 1849
       1.1.3.1 Family Prochloraceae Lewin (1977), nom. inval. [monotypic] see Family Prochloraceae Lewin ex Florenzano, Balloni & Materassi (1986), nom. inval.
       1.1.3.2 Family Gomphosphaeriaceae Elenkin (1933) [monotypic] see Family Gomphosphaeriaceae Elenkin 1933
       1.1.4 Family Pleurocapsaceae Geitler (1925) see Family Hyellaceae Borzì (1914)
       1.2 Family Chroococcaceae Nägeli (1849) see Family Chroococcaceae Nägeli 1849
       2 Family Halothecaceae Strunecký & Mareš (2023) see Family Halothecaceae Strunecký and Mareš 2023