• Adrianema adriaticum (Ercegovic) G.De Toni, 1936
• Aeolisaccus barattoloi De Castro, 1989 † accepted as Decastronema barattoloi (De Castro) Golubic, Radoicic & S.-J.Lee, 2008 †
• Aeolisaccus dunningtonii G.F.Elliott (uncertain)
• Aetokthonos hydrillicola S.B.Wilde & J.R.Johansen, 2014
• Albrightia roraimae Kastovský, Fucíková, Hauer & Bohunická, 2011
• Albrightia tortuosa J.Copeland, 1936
• Aliinostoc morphoplasticum Bagchi, Dubey & P.Singh, 2017
• Amphiheterocytum lacustre Sant'Anna et al., 2018
• Amphithrix amethystea (Kützing) Kützing, 1849 (uncertain)
• 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 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 Borge, 1906
• Anabaena aequalis f. anomala Kossinska [Kossinskaya], 1932
• 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. 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. 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 f. cylindrospora Kiselev (uncertain)
• Anabaena arctica f. ovospora Kiselev (uncertain)
• Anabaena arctica var. recta Kiselev (uncertain)
• Anabaena arctica var. spiroides Kiselev (uncertain)
• Anabaena arenicola (Kützing) Trevisan, 1845 (uncertain)
• Anabaena aspera Frémy, 1930
• Anabaena attenuata Kiselev, 1940
• Anabaena augstumalis Schmidle, 1900
• Anabaena augstumnalis Schmidle, 1900
• Anabaena augstumnalis f. incrassata (Nygaard) Elenkin (uncertain)
• Anabaena augstumnalis var. incrassata (Nygaard) Geitler, 1932 accepted as Dolichospermum sigmoideum (Nygaard) Wacklin, L.Hoffmann & Komárek, 2009
• Anabaena augstumnalis var. longispora Tarnavschi & Mitroiu, 1956 (uncertain)
• Anabaena australica Playfair, 1918
• Anabaena australica var. constricta Playfair
• Anabaena austro-africana 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 E.J.Schmidt, 1899
• Anabaena batophora Frémy, 1930
• Anabaena beckii G.De Toni, 1935
• Anabaena bederi Seckt
• Anabaena belmontica C.G.M.Archibald, 1967
• Anabaena berezowskii Usacev, 1928 accepted as Dolichospermum berezowskii (Usacev) Wacklin, L.Hoffmann & Komárek, 2009
• Anabaena bergii Ostenfeld, 1908 accepted as Chrysosporum bergii (Ostenfeld) E.Zapomelová, O.Skácelová, P.Pumann, R.Kopp & E.Janecek, 2012
• Anabaena bergii var. affinis (Lemmermann) Geitler (uncertain)
• Anabaena bergii var. limnetica Couté & Preisig accepted as Anabaena minderi Huber-Pestalozzi, 1938
• Anabaena bergii var. minor Kisselev, 1927 accepted as Chrysosporum minus (Kiselev) Komárek, 2012
• Anabaena berkeleyana Batters, 1902
• Anabaena bernardinensis Chodat & Zender, 1924
• Anabaena bharadwajae B.N.Prasad, 1951
• Anabaena bispora Gayral & Mazancourt, 1958
• Anabaena bituri Cronberg & Komárek, 2004 accepted as Dolichospermum bituri (Cronberg & Komárek) P.Wacklin, L.Hoffmann & J.Komárek, 2009
• Anabaena bonariensis Seckt, 1922
• Anabaena borealis E.Larsen, 1907 (uncertain)
• Anabaena bornetiana F.S.Collins, 1896
• Anabaena bothae H.Welsh, 1961 accepted as Dolichospermum bothae (H.Welsh) Wacklin, L.Hoffmann & Komárek, 2009
• Anabaena botulus Margalef, 1951 accepted as Trichormus botulus (Margalef) Komárek & Anagnostidis, 1989
• Anabaena brevis Kützing, 1845 (uncertain)
• Anabaena broomei Batters, 1891
• Anabaena bullosa Kützing, 1843 accepted as Fischerella laminosa (Hansgirg ex Bornet & Flahault) Castenholz accepted as Mastigocladus laminosus Cohn ex Kirchner, 1898
• Anabaena calcicola C.Agardh ex Fries, 1835 accepted as Schizothrix calcicola Gomont, 1892
• Anabaena calida Kützing, 1849 (uncertain)
• Anabaena californica O.Borge, 1909 accepted as Anabaena inaequalis Bornet & Flahault, 1886
• Anabaena carmichaelii Cronberg & Komárek, 2004
• Anabaena caspica Ostenfeld, 1901 accepted as Dolichospermum caspicum (Ostenfeld) Wacklin, Hoffmann & Komárek, 2009
• Anabaena catenula Kützing ex Bornet & Flahault, 1886
• Anabaena catenula var. affinis (Lemmermann) Geitler, 1932 accepted as Dolichospermum affine (Lemmermann) Wacklin, L.Hoffmann & Komárek, 2009
• Anabaena catenula var. africana O.Borge, 1928
• Anabaena catenula var. intermedia Griffiths ex Geitler, 1932 accepted as Dolichospermum danicum (Nygaard) P.Wacklin, L.Hoffmann & J.Komárek, 2009
• Anabaena catenula var. minor V.K.Laloraya & A.K.Mitra, 1971 accepted as Trichormus minor (V.K.Laloraya & A.K.Mitra) J.Komárek & K.Anagnostidis, 1989
• Anabaena catenula var. solitaria (Klebahn) Geitler, 1932 accepted as Dolichospermum solitarium (Klebahn) Wacklin, L.Hoffmann & Komárek, 2009
• Anabaena cavanillesiana González Guerrero, 1946
• Anabaena chalybea Kützing, 1843 (uncertain)
• Anabaena chalybea var. amethystea Kützing (uncertain)
• Anabaena chalybea var. ligustica Piccone (uncertain)