• 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 †
• Aerosakkonema funiforme Nanda Kyaw Thu & Watanabe, 2012
• Affixifilum floridanum Lefler, D.E.Berthold & Laughinghouse, 2021
• Affixifilum granulosum (Caires, Sant'Anna & Nunes) Lefler, D.E.Bertholdt & Laughinghouse, 2021
• Alborzia kermanshahica Nowruzi & F.Soares, 2021
• 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
• 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
• Ammatoidea xizangensis Zhu & Y.-Y.Li, 1984
• Ammatoidea yellowstonensis J.J.Copeland, 1936
• Anabaeniolum longum Nadson & Krassilnikov (uncertain)
• Anacystis amplivesiculata N.L.Gardner, 1927
• Anacystis anaptis B.Biswal, Panigrahi & U.Biswal, 1980
• Anacystis anomala N.L.Gardner, 1927
• Anacystis botryoides (Linnaeus) Meneghini, 1837 (uncertain)
• Anacystis brunnea (A.Braun ex Kützing) Wolle, 1887 accepted as Aphanocapsa brunnea (A.Baun ex Kützing) Nägeli, 1849
• Anacystis compacta N.L.Gardner, 1927
• Anacystis consociata N.L.Gardner, 1927
• Anacystis cyanea (Kützing) F.E.Drouet & W.A.Daily, 1952 accepted as Microcystis aeruginosa (Kützing) Kützing, 1846
• Anacystis cylindracea N.L.Gardner, 1927 accepted as Aphanothece cylindracea (N.L.Gardner) Komárek & Anagnostidis, 1995
• Anacystis dimidiata (Kützing) Drouet & Daily, 1952 accepted as Chroococcus turgidus (Kützing) Nägeli, 1849
• Anacystis distans N.L.Gardner, 1927
• Anacystis firma (Kützing) F.E.Drouet & W.A.Daily, 1948 accepted as Microcystis firma (Kützing) Schmidle, 1902
• Anacystis furfuracea (Berkeley) Meneghini, 1842
• Anacystis gigas (West & G.S.West) N.L.Gardner, 1927 accepted as Gloeocapsa gigas West & G.S.West, 1894
• Anacystis glauca Wolle, 1877 accepted as
• Anacystis gloeocapsoides Gardner, 1927
• Anacystis grevillei (Berkeley) Kützing, 1849 accepted as Aphanocapsa grevillei (Berkeley) Rabenhorst, 1865
• Anacystis hyalina H.-J.Chu, 1944 accepted as Asterocapsa hyalina (H.-J.Chu) H.-J.Chu, 1952
• Anacystis incerta (Lemmermann) Drouet & Daily, 1952 accepted as Aphanocapsa incerta (Lemmermann) G.Cronberg & Komárek, 1994
• Anacystis irregularis N.L.Gardner, 1927
• Anacystis magnifica N.L.Gardner, 1927 accepted as Asterocapsa magnifica (N.L.Gardner) Komárek, 1993
• Anacystis marginata Meneghini, 1837 accepted as Microcystis marginata (Meneghini) Kützing, 1846
• Anacystis marina (Hansgirg) Drouet & Daily, 1948 accepted as Aphanocapsa marina Hansgirg, 1890
• Anacystis microsphaeria N.L.Gardner, 1927
• Anacystis minuta (C.Agardh) Meneghini, 1842
• Anacystis minutissima N.L.Gardner, 1927
• Anacystis montana (Lightfoot) Drouet & Daily, 1952 accepted as Gloeocapsa atrata Kützing, 1843
• Anacystis montana f. gelatinosa Drouet & Daily, 1956 (uncertain)
• Anacystis montana f. minor F.E.Drouet & W.A.Daily
• Anacystis nidulans N.L.Gardner, 1927 accepted as Asterocapsa nidulans (N.L.Gardner) Komárek & Komárková-Legnerová, 2007
• Anacystis nigropurpurea N.L.Gardner, 1927
• Anacystis nigroviolacea N.L.Gardner, 1927
• Anacystis paludosa Rabenhorst, 1865 (uncertain)
• Anacystis peniocystis (Kützing) F.E.Drouet & W.A.Daily, 1942 accepted as Gloeocapsa peniocystis Kützing, 1847
• Anacystis pulchra N.L.Gardner, 1927 accepted as Asterocapsa pulchra (N.L.Gardner) Komárek, 1993
• Anacystis pulvereus (Wood) Wolle, 1887 accepted as Microcystis pulverea (H.C.Wood) Forti, 1907
• Anacystis purpurea C.-C.Jao, 1944 accepted as Asterocapsa purpurea (C.-C.Jao) H.-J.Chu, 1952
• Anacystis radiata N.L.Gardner, 1927
• Anacystis radiata var. major N.L.Gardner, 1927
• Anacystis reinboldii Richter, 1891 accepted as Aphanocapsa reinboldii (Richter) Komárek & Anagnostidis, 1995
• Anacystis roeseana (De Bary) Drouet & Daily, 1948 (uncertain)
• Anacystis rupestris (Lyngbye) F.E.Drouet & W.A.Daily, 1942 accepted as Gloeothece rupestris (Lyngbye) Bornet, 1880
• Anacystis rupestris var. prasina (A.Braun) F.E.Drouet & W.A.Daily, 1942 accepted as Aphanothece stagnina (Sprengel) A.Braun, 1863
• Anacystis thermalis (Meneghini) Drouet & Daily, 1952
• Anacystis thermalis f. major (Lagerheim) Drouet & Daily, 1956 accepted as Chroococcus limneticus Lemmermann, 1898 accepted as Limnococcus limneticus (Lemmermann) Komárková, Jezberová, O.Komárek & Zapomelová, 2010
• Anacystis trochiscioides C.-C.Jao, 1944 accepted as Asterocapsa trochiscioides (C.-C.Jao) H.-J.Chu, 1952
• Anacystis willei N.L.Gardner, 1927
• Ancylothrix rivularis M.D.Martins & L.H.Z.Branco, 2016
• Ancylothrix terrestris M.D.Martins & L.H.Z.Branco, 2015
• Angulocellularia anisotoma Vologdin, 1962 †
• Angulocellularia mansurkaensis Vologdin, 1962 †
• Annamia dubia Tuji, H.Yamaguchi & Niiyama, 2021
• Annamia toxica Nguyen, 2013
• Aphanocapsa albida Zeller, 1873
• Aphanocapsa annulata G.B.McGregor, 2007
• Aphanocapsa anodontae Hansgirg, 1893 accepted as Aphanocapsa rivularis (Carmichael) Rabenhorst, 1865
• Aphanocapsa arctica Whelden, 1947
• Aphanocapsa aurantia (C.Agardh) Rabenhorst, 1865 accepted as Chroococcus aurantius (C.Agardh) Wille, 1918
• Aphanocapsa banaresensis Bharadwaja, 1935
• Aphanocapsa benaresensis Bharadwaja, 1935
• Aphanocapsa biformis A.Braun, 1879
• Aphanocapsa botryoides J.J.Copeland, 1936
• Aphanocapsa brunnea (A.Baun ex Kützing) Nägeli, 1849
• Aphanocapsa castagnei (Kützing) Rabenhorst, 1865 accepted as Aphanothece castagnei (Kützing) Rabenhorst, 1865
• Aphanocapsa concharum Hansgirg, 1890
• Aphanocapsa conferta (West & G.S.West) Komárková-Legnerová & Cronberg, 1994
• Aphanocapsa crassa Ghose, 1927
• Aphanocapsa cruenta (Smith) Hansgirg, 1885 accepted as Porphyridium purpureum (Bory) K.M.Drew & R.Ross, 1965
• Aphanocapsa cruenta var. wittrockii (Richter) Hansgirg, 1893 accepted as Porphyridium wittrockii Richter, 1882
• Aphanocapsa cumulus Komárek & Cronberg, 1999
• Aphanocapsa delicatissima West & G.S.West, 1912
• Aphanocapsa depressa (Berkeley) Rabenhorst, 1865
• Aphanocapsa dharwadensis Bongale, 1987