• Abruptophycus compositus Vologdin, 1962 †
• Acaciella angepena W.V.Preiss, 1972 †
• Acaciella augusta W.V.Preiss, 1972 †
• Acaciella australica (Howchin) M.R.Walter, 1972 †
• Acaciella savoryensis K.Grey & M.R.Walter, 1994 †
• Acanthina bullosa Korde, 1973 †
• Acanthina multiformis Korde, 1973 †
• Acaryochloris marina H.Miyashita & Chihara, 2003 (uncertain)
• Acaryochloris thomasi Partensky & al., 2018
• Achroonema angustum (Koppe) Skuja, 1956 accepted as Oscillatoria angusta Koppe, 1924
• Achroonema articulatum Skuja, 1956
• Achroonema gotlandicum Skuja, 1956
• Achroonema inaequale Skuja, 1956
• Achroonema lentum Skuja, 1956
• Achroonema macromeres Skuja, 1956
• Achroonema minimum G.S.An, 1992 accepted as Pseudanabaena minima (G.S.An) Anagnostidis, 2001
• Achroonema proteiforme Skuja, 1956
• Achroonema simplex Skuja, 1956
• Achroonema spiroideum Skuja, 1948
• Achroonema splendens Skuja, 1956
• Achroonema splendens f. tenuior Skuja (uncertain)
• Achroonema sporogenum Skuja, 1956
• Achroonema subsalsum Behre (uncertain)
• Actinophycus kordeae Vologdin, 1962 †
• Actinophycus obrutschevii Korde, 1954 †
• Actinophycus parvus Vologdin, 1962 †
• Actinophycus ramosus Vologdin, 1962 †
• Actinothorax stokesiana (J.E.Gray) J.E.Gray accepted as Actinothrix stokesiana J.E.Gray, 1864
• Actinothrix stokesiana J.E.Gray, 1864 (uncertain)
• Acuasiphonoria ordovica Lijing Liu, Yasheng Wu, H.J.Yang & Riding, 2016 †
• Adrianema adriaticum (Ercegovic) G.De Toni, 1936
• Aegeococcus anagnostidisii Konstantinou & Gkelis, 2020
• Aegeococcus thuretii Konstantinou & Gkelis, 2020
• Aerofilum fasciculatum Chakraborty & J.Mukherjee, 2021
• Aerosakkonema funiforme Nanda Kyaw Thu & Watanabe, 2012
• Aetokthonos hydrillicola S.B.Wilde & J.R.Johansen, 2014
• Affixifilum floridanum Lefler, D.E.Berthold & Laughinghouse, 2021
• Affixifilum granulosum (Caires, Sant'Anna & Nunes) Lefler, D.E.Bertholdt & Laughinghouse, 2021
• Agmenellum prasiola (Meneghini) Brébisson, 1839 accepted as Trochiscia prasiola Meneghini, 1837
• Agmenellum quadrijugum (Turpin) Trevisan, 1842 (uncertain)
• Agmenellum quadruplicatum (Meneghini) Brébisson, 1839 accepted as Merismopedia quadruplicata (Meneghini) Trevisan, 1845
• Agmenellum thermale (Kützing) Drouet & Daily, 1956 accepted as Merismopedia thermalis Kützing, 1843
• Agmenellum tranquillum (Ehrenberg) Trevisan, 1842 accepted as Merismopedia tranquilla (Ehrenberg) Trevisan, 1845
• Ainactis alpina Kützing (uncertain)
• Albertania alaskensis Strunecky, Raabova, Bernardova, Ivanova, Semanova, Crossley & Kaftan, 2019
• Albertania obscura R.F.S.Luz, Kaštovský, J.R.Johansen & V.Gonçalves, 2023
• Albertania pratii J.R.Johansen, Kaštovský & M.U. Akagha, 2023
• Albertania skiophila Zammit, 2018
• Alborzia kermanshahica Nowruzi & F.Soares, 2021
• Albrightia roraimae Kastovský, Fucíková, Hauer & Bohunická, 2011
• Albrightia tortuosa J.Copeland, 1936
• Alcheringa narrina M.R.Walter, 1972 †
• Aliinostoc alkaliphilum Christodoulou, Economou-Amilli, M.Fiore & Sivonen, 2022
• Aliinostoc bakau Merican, Abdul Rahim, Broady, Convey & Muangmai, 2023
• Aliinostoc catenatum Kabirnataj, Nematzadeh, Talebi, Saraf, Suradkar, Tabatabaei & Singh, 2020
• Aliinostoc constrictum Kabirnataj et al., 2020 accepted as Pseudoaliinostoc constrictum (Kabirnataj & al.) Lee, N.-J., Bang, S.-D., Kim, T., Ki., J.-S. & Lee, O.-M., 2021
• Aliinostoc magnakinetifex Kabirnataj, Nematzadeh, Talebi, Saraf, Suradkar, Tabatabaei & Singh, 2020
• Aliinostoc morphoplasticum Bagchi, Dubey & P.Singh, 2017
• Aliinostoc soli A.Saraf & al., 2018 † accepted as Pseudoaliinostoc soli (A.Saraf & al.) Lee, Bang, Kim, Ki & Lee, 2021 †
• Aliinostoc tiwarii A.Saraf, P.Singh & al., 2018 accepted as Pseudoaliinostoc tiwarii (A.Saraf, P.Singh & al.) Lee, Bang, Kim, Ki & Lee, 2021
• Aliinostoc vietnamicum S.Maltseva, E.Kezlya & Y.Maltsev, 2022
• Aliterella antarctica J.Rigonato et al., 2016
• Aliterella atlantica J.Rigonato et al., 2016 (uncertain)
• Aliterella chasmolithica P.Jung, Schermer, Mikhailyuk & Büdel, 2020
• Aliterella compacta P.Jung, Büdel & Lakatos, 2021
• Aliterella gigantea P.Jung, Büdel & Lakatos, 2021
• Aliterella shaanxiensis unknon authority (uncertain)
• Aliterella vladivostokensis Abdullin, A.Y.Nikulin, Bagmet & V.Y.Nikulin, 2021
• Alkalinema pantanalense Vieira Vaz et al., 2015
• Allocoleopsis franciscana Moreira-Fernandes, Giraldo-Silva, D.Roush & Garcia-Pichel, 2021
• Alpinella graeca Dragastan, Gieslich, D.K.Richter, Grewer, Kaziur, Kube & Radusch, 1994 †
• Altericista lacusladogae Averina, E.Polyakova, Senetskaya & Pinevich, 2021
• Altericista variichlora Averina, E. Polyakova, Senatskaya & Pinevich, 2021
• Altericista violacea Averina, E.Polyakova, Senatskaya & Pinevich, 2021
• Alternantia geitleri J.Schiller, 1954
• Alternantia quadriga J.Schiller, 1954
• Alternantia ramifera J.Schiller, 1954
• Alternantia serra J.Schiller, 1954
• Alternantia tabularis J.Schiller, 1954
• Alternella bianca (Raaben) Raaben, 1972 †
• Alternella hyperboreica Raaben, 1972 †
• Alternia silva Vologdin, 1962 †
• Amalia elegans (Wołoszyńska) De Toni, 1934 accepted as Romeria elegans (Woloszynska) Geitler, 1932
• Amalia gracilis (Koczwara) G.B.De Toni, 1934 accepted as Romeria gracilis (Koczwara) Koczwara, 1932
• Amalia leopoliensis (Raciborski) De Toni, 1934 accepted as Romeria leopoliensis (Raciborski) Koczwara, 1932
• Amazoninema brasiliense Genuário, W.R.de Souza, R.T.R.Monteiro, Sant'Anna & I.T.S.Melo, 2020
• Amazonocrinis nigriterrae Alvarenga & al., 2021
• Amazonocrinis thailandica Tawong, Pongcharoen, Pongpadung, Ponza & Saijuntha, 2022
• Ambigolamellatus ovatus Maithy, 1979 †
• Amganella glabra (Vologdin) Reitlinger, 1959 † accepted as Proaulopora glabra Vologdin, 1938 †
• Ammassolinea attenuata P.Hasler, P.Dvorák, A.Poulícková & D.A.Casamatta, 2014
• Ammatoidea aegaea Anagnostidis & Pantazidou, 1991
• Ammatoidea breviarticulata Hirose & Chung, 1970
• Ammatoidea multispora Yoneda, 1952
• Ammatoidea murmanica Petrov, 1961
• Ammatoidea normanii West & G.S.West, 1897
• Ammatoidea olivacea Yoneda, 1952
• Ammatoidea simplex Woronichin, 1923
• Ammatoidea sinensis S.-H.Ley, 1944
• Ammatoidea singularis Hirose & Chung, 1970