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
     1 Order Gloeobacterales Caval.-Sm. (2002), nom. inval. see Order Gloeobacterales Cavalier-Smith 2002 nom. inval., nom. rej.
     2.1.1 Order Aegeococcales Strunecký & Mareš (2023) [monotypic] see Order Aegeococcales Strunecký and Mareš 2023
     2.1.2 Order Thermostichales Komárek & Strunecký (2020) [monotypic] see Order Thermostichales Komárek and Strunecký 2020
     2.2.1 Order Pseudanabaenales L. Hoffm., Komárek & Kaštovský (2005), nom. inval. see Order Pseudanabaenales Hoffmann et al. 2005 nom. nud.
     2.2.2.1 Order Gloeomargaritales Moreira, Tavera, Benzerara, Skouri-Panet, Couradeau, Gérard, Fonta, Novelo, Zivanovic & López-García (2017) [monotypic] see Order Gloeomargaritales Moreira et al. 2017
     2.2.2.2.1 Order Acaryochloridales Strunecký & Mareš (2023), nom. inval. see Order Acaryochloridales Strunecký and Mareš 2023 nom. inval.
     2.2.2.2.2.1.1.1 Order Prochlorotrichales Strunecký & Mareš (2023) [monotypic] see Order Prochlorotrichales Strunecký and Mareš 2023
     2.2.2.2.2.1.1.2 Order Synechococcales Hoffmann, Komárek & Kaštovský (2005), nom. inval. see Order Synechococcales Hoffmann et al. 2005 nom. nud.
     2.2.2.2.2.1.2 Order Nodosilineales Strunecký & Mareš (2023) see Order Nodosilineales Strunecký and Mareš 2023
     2.2.2.2.2.2.1 Order Leptolyngbyales Strunecký & Mareš (2023) [paraphyletic] see Order Leptolyngbyales Strunecký and Mareš 2023
     2.2.2.2.2.2.1.2.2.2 Order Oculatellales Strunecký & Mareš (2023) [monotypic] see Order Oculatellales Strunecký and Mareš 2023
     2.2.2.2.2.2.1.2.3.1 Order Geitlerinematales Strunecký & Mareš (2023) [monotypic] see Order Geitlerinematales Strunecký and Mareš 2023
     2.2.2.2.2.2.1.2.3.2.1 Order Desertifilales Strunecký & Mareš (2023) [monotypic] see Order Desertifilales Strunecký and Mareš 2023
     2.2.2.2.2.2.1.2.3.2.2 Order Oscillatoriales Schaffner (1922) see Order Oscillatoriales Schaffner 1922
     2.2.2.2.2.2.1.2.3.2.3.1.1 Order Coleofasciculales Strunecký & Mareš (2023) see Order Coleofasciculales Strunecký and Mareš 2023
     2.2.2.2.2.2.1.2.3.2.3.1.2.1 Order Spirulinales Komárek, J. Kaštovský, J. Mareš & J.R.Johans. (2014) see Order Spirulinales Komárek et al. 2014
     2.2.2.2.2.2.1.2.3.2.3.1.2.2 Order Chroococcales Ardissone (1887) see Order Chroococcales corrig. Ardissone 1887
     2.2.2.2.2.2.1.2.3.2.3.2 Order Gomontiellales Strunecký & Mareš (2023) see Order Gomontiellales Strunecký and Mareš 2023
     2.2.2.2.2.2.1.2.3.2.3.3.1 Order Chroococcidiopsidales Komárek, J. Kaštovský, J. Mareš & J.R.Johans. (2014) [monotypic] see Order Chroococcidiopsidales Komárek et al. 2014
     2.2.2.2.2.2.1.2.3.2.3.3.2 Order Nostocales Borzì (1914) see Order Nostocales corrig. Borzì 1914