• Actinophycus kordeae Vologdin, 1962 †
• Actinophycus obrutschevii Korde, 1954 †
• Actinophycus parvus Vologdin, 1962 †
• Actinophycus ramosus Vologdin, 1962 †
• Adrianema adriaticum (Ercegovic) G.De Toni, 1936
• Aetokthonos hydrillicola S.B.Wilde & J.R.Johansen, 2014
• Ainactis alpina Kützing (uncertain)
• Albrightia roraimae Kastovský, Fucíková, Hauer & Bohunická, 2011
• Albrightia tortuosa J.Copeland, 1936
• 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
• Alpinella graeca Dragastan, Gieslich, D.K.Richter, Grewer, Kaziur, Kube & Radusch, 1994 †
• Alternia silva Vologdin, 1962 †
• Amazonocrinis nigriterrae Alvarenga & al., 2021
• Amazonocrinis thailandica Tawong, Pongcharoen, Pongpadung, Ponza & Saijuntha, 2022
• Amganella glabra (Vologdin) Reitlinger, 1959 † accepted as Proaulopora glabra Vologdin, 1938 †
• Amorphonostoc entophytum (Bornet & Flahault) Elenkin, 1936 accepted as Nostoc paludosum Kützing ex Bornet & Flahault, 1886
• Amorphonostoc paludosum (Kützing ex Bornet & Flahault) Elenkin, 1936 accepted as Nostoc paludosum Kützing ex Bornet & Flahault, 1886
• Amorphonostoc punctiforme (Hariot) Elenkin, 1936 accepted as Nostoc paludosum Kützing ex Bornet & Flahault, 1886
• Amorphonostoc punctiforme (Kützing) Elenkin (uncertain)
• Amorphonostoc punctiforme f. polymorphum Kukk accepted as Nostoc commune Vaucher ex Bornet & Flahault, 1888
• Amorphonostoc punctiforme f. populorum (Geitler) Hollerbach, 1936 accepted as Nostoc punctiforme f. populorum (Geitler) Hollerbach, 1936
• Amorphonostoc symbioticum (F.Wettstein) Elenkin, 1936 accepted as Nostoc symbioticum F.V.Wettstein, 1915
• Amphiheterocytum lacustre Sant'Anna et al., 2018
• Amphithrix amethystea (Kützing) Kützing, 1849 accepted as Schizothrix calcicola Gomont, 1892
• Amphithrix amoena Kützing, 1843 accepted as Phormidium ambiguum Gomont, 1892
• Amphithrix barbata Kützing, 1847 (uncertain)
• Amphithrix hospita Kützing, 1849 accepted as Dasyactis hospita (Kützing) P.L.Crouan & H.M.Crouan, 1867
• Amphithrix incrustata Kützing, 1847 (uncertain)
• Amphithrix janthina Bornet & Flahault, 1886 accepted as Tapinothrix janthina (Bornet & Flahault) Bohunická & J.R.Johansen, 2011
• Amphithrix janthina f. torulosa (Bornet & Flahault) Elenkin, 1949 accepted as Amphithrix janthina var. torulosa Bornet & Flahault, 1886
• Amphithrix janthina var. torulosa Bornet & Flahault, 1886
• Amphithrix laminariae Kuckuck, 1894 accepted as Tapinothrix violacea Bohunická & J.R.Johansen, 2011
• Amphithrix leprieurei Montagne, 1861 (uncertain)
• Amphithrix meneghiniana Kützing, 1843 (uncertain)
• Amphithrix papillosa Rabenhorst, 1863 accepted as Arthrotilum papillosum (Rabenhorst) Rabenhorst, 1865
• Amphithrix rudis (Meneghini) Kützing, 1849 accepted as Arthrotilum rude (Meneghini) Rabenhorst, 1865
• Amphithrix sargassi P.L.Crouan & H.M.Crouan, 1865 (uncertain)
• Amphithrix scytonemoidea (Meneghini) Trevisan, 1845 (uncertain)
• Amphithrix thermalis Kützing, 1849 accepted as Arthrotilum thermale (Kützing) Rabenhorst, 1865
• Amphithrix villosa Kützing, 1845 (uncertain)
• Amphithrix violacea Bornet & Flahault, 1886 accepted as Tapinothrix violacea Bohunická & J.R.Johansen, 2011
• Anabaena abnormis Proskina-Lavrenko & Makarova, 1968
• Anabaena aequalis O.Borge, 1906
• Anabaena aequalis f. anomala Kossinskaja, 1932
• Anabaena aequalis f. major (Aptekar) Elenkin, 1938 accepted as Anabaena aequalis var. major Aptekar, 1928
• Anabaena aequalis var. major Aptekar, 1928
• Anabaena aequalis var. unispora V.Das & Mitra (uncertain)
• Anabaena aerophila Brabez, 1941
• Anabaena aeruginosa N.L.Gardner, 1927
• Anabaena affinis Lemmermann, 1898 accepted as Dolichospermum affine (Lemmermann) Wacklin, L.Hoffmann & Komárek, 2009
• Anabaena affinis f. viguieri (Denis & Frémy) Komérek, 1958 accepted as Dolichospermum viguieri (Denis & Frémy) Wacklin, L.Hoffmann & Komárek, 2009
• Anabaena affinis var. holsatica Lemmermann, 1903 accepted as Dolichospermum affine (Lemmermann) Wacklin, L.Hoffmann & Komárek, 2009
• Anabaena affinis var. intermedia B.M.Griffiths, 1925 accepted as Dolichospermum danicum (Nygaard) P.Wacklin, L.Hoffmann & J.Komárek, 2009
• Anabaena alatospora Gonzalvez & Kamat, 1959
• Anabaena allahabadii A.K.Mitra, 1951
• Anabaena allantospora Montagne, 1846 (uncertain)
• Anabaena ambigua C.B.Rao, 1937 accepted as Wollea ambigua (C.B.Rao) R.Y.Singh, 1942
• Anabaena ambigua var. limayensis Guarrera, 1995
• Anabaena ambigua var. minor (Ley.) Fritsch (uncertain)
• Anabaena anisococca (Sprengel) Trevisan, 1845 accepted as Nostoc anisococcum Sprengel, 1827
• Anabaena anisococca Migula, 1905
• Anabaena anomala F.E.Fritsch, 1949 accepted as Trichormus anomalus (F.E.Fritsch) Komárek & Anagnostidis, 1989
• Anabaena antarctica F.E.Fritsch, 1912 accepted as Trichormus antarcticus (F.E.Fritsch) Komárek & Anagnostidis, 1989
• Anabaena aphanizomenoides Forti, 1911 accepted as Sphaerospermopsis aphanizomenoides (Forti) Zapomelová, Jezberová, Hrouzek, Hisem, Reháková & Komárková, 2010
• Anabaena arctica Kisselev, 1932 accepted as Dolichospermum arcticum (Kiselev) P.Wacklin, L.Hoffmann & J.Komárek, 2009
• Anabaena arctica f. cylindrospora Kisselev (uncertain)
• Anabaena arctica f. ovospora Kisselev (uncertain)
• Anabaena arctica var. recta Kisselev (uncertain)
• Anabaena arctica var. spiroides Kisselev (uncertain)
• Anabaena arenicola (Kützing) Trevisan, 1845 (uncertain)
• Anabaena aspera Frémy, 1930
• Anabaena attenuata Kisselev, 1940
• Anabaena augstumalis Schmidle, 1900
• Anabaena augstumalis f. incrassata (Nygaard) Elenkin accepted as Dolichospermum sigmoideum (Nygaard) Wacklin, L.Hoffmann & Komárek, 2009
• Anabaena augstumalis f. marchica (Lemmermann) Elenkin accepted as Anabaena augstumalis var. marchica Lemmermann, 1905
• Anabaena augstumalis var. incrassata (Nygaard) Geitler, 1932 accepted as Dolichospermum sigmoideum (Nygaard) Wacklin, L.Hoffmann & Komárek, 2009
• Anabaena augstumalis var. longispora Tarnavschi & Mitroiu, 1956 (uncertain)
• Anabaena augstumalis var. marchica Lemmermann, 1905
• Anabaena augstumnalis Schmidle, 1900
• Anabaena augstumnalis var. longispora Tarnavschi & Mitroiu, 1956 (uncertain)
• Anabaena australica Playfair, 1918
• Anabaena australica var. constricta Playfair
• Anabaena austroafricana Cronberg & Komárek, 2004
• Anabaena azollae Strasburger, 1884 accepted as Trichormus azollae (Strasburger) Komárek & Anagnostidis, 1989
• Anabaena azotica Ley, 1959
• Anabaena ballygungii Banerji, 1938 accepted as Anabaenopsis ballygungii (Banerji) Komárek & Anagnostidis, 1989
• Anabaena baltica Johs.Schmidt, 1899 accepted as Anabaena spiroides f. baltica (Johs.Schmidt) Pankow, 1965
• Anabaena batophora Frémy, 1930
• Anabaena beckii G.De Toni, 1935
• Anabaena bederi Seckt
• Anabaena belmontica C.G.M.Archibald, 1967
• Anabaena berezowskii Usačev, 1928 accepted as Dolichospermum berezowskii (Usacev) Wacklin, L.Hoffmann & Komárek, 2009