• Achroonema lentum Skuja, 1956
• Achroonema proteiforme Skuja, 1956
• Agmenellum quadruplicatum (Meneghini) Brébisson, 1839 accepted as Merismopedia quadruplicata (Meneghini) Trevisan, 1845
• Ammatoidea aegaea Anagnostidis & Pantazidou, 1991
• Anabaena aequalis O.Borge, 1906
• Anabaena baltica Johs.Schmidt, 1899 accepted as Anabaena spiroides f. baltica (Johs.Schmidt) Pankow, 1965
• Anabaena circinalis Rabenhorst ex Bornet & Flahault, 1886 accepted as Dolichospermum sigmoideum (Nygaard) Wacklin, L.Hoffmann & Komárek, 2009
• Anabaena constricta (Szafer) Geitler, 1925 accepted as Johanseninema constrictum (Szafer) Hasler, Dvorák & Poulícková, 2014
• Anabaena crassa (Lemmermann) Komárková-Legnová & Cronberg, 1992 accepted as Dolichospermum crassum (Lemmermann) Wacklin, Hoffmann & Komárek, 2009
• Anabaena cylindrica Lemmermann, 1896
• Anabaena echinospora Skuja, 1926
• Anabaena flos-aquae Brébisson ex Bornet & Flauhault, 1886 accepted as Dolichospermum flos-aquae (Bornet & Flahault) P.Wacklin, L.Hoffmann & Komárek, 2009
• Anabaena hassallii Wittrock ex Lemmermann, 1907 accepted as Dolichospermum circinale (Rabenhorst ex Bornet & Flahault) P.Wacklin, L.Hoffmann & J.Komárek, 2009
• Anabaena inaequalis Bornet & Flahault, 1886
• Anabaena laxa A.Braun, 1886
• Anabaena lemmermannii P.G.Richter, 1903 accepted as Dolichospermum lemmermannii (Richter) P.Wacklin, L.Hoffmann & J.Komárek, 2009
• Anabaena oscillarioides Bory ex Bornet & Flahault, 1886
• Anabaena perturbata H.Hill, 1976 accepted as Dolichospermum perturbatum (H.Hill) Wacklin, L.Hoffmann & Komárek, 2009
• Anabaena planctonica Brunnthaler, 1903 accepted as Dolichospermum planctonicum (Brunnthaler) Wacklin, L.Hoffmann & Komárek, 2009
• Anabaena pseudoscillatoria Bory de Saint-Vincent, 1822 accepted as Anabaena oscillarioides Bory ex Bornet & Flahault, 1886
• Anabaena sphaerica Bornet & Flahault, 1886
• Anabaena spiroides Klebahn, 1895 accepted as Dolichospermum spiroides (Klebhan) Wacklin, L.Hoffmann & Komárek, 2009
• Anabaena spiroides f. baltica (Johs.Schmidt) Pankow, 1965
• Anabaena spiroides f. crassa (Lemmerman) Elenkin, 1938 accepted as Dolichospermum crassum (Lemmermann) Wacklin, Hoffmann & Komárek, 2009
• Anabaena spiroides f. hassallii Pankow, 1965 accepted as Dolichospermum circinale (Rabenhorst ex Bornet & Flahault) P.Wacklin, L.Hoffmann & J.Komárek, 2009
• Anabaena spiroides var. crassa Lemmermann, 1898 accepted as Dolichospermum crassum (Lemmermann) Wacklin, Hoffmann & Komárek, 2009
• Anabaena torulosa Lagerheim ex Bornet & Flahault, 1886
• Anabaena variabilis Kützing ex Bornet & Flahault, 1886 accepted as Trichormus variabilis (Kützing ex Bornet & Flahault) Komárek & Anagnostidis, 1989
• Anabaenopsis arnoldii Aptekar, 1926
• Anabaenopsis circularis (G.S.West) V.V.Miller, 1923
• Anabaenopsis elenkinii V.V.Miller, 1923
• Anabaenopsis milleri Woronichin, 1929
• Anabaenopsis tanganyikae (G.S.West) V.V.Miller, 1923
• Anacystis dimidiata (Kützing) Drouet & Daily, 1952 accepted as Chroococcus turgidus (Kützing) Nägeli, 1849
• Anacystis marina (Hansgirg) Drouet & Daily, 1948 accepted as Aphanocapsa marina Hansgirg, 1890
• Anagnostidinema acutissimum (Kufferath) Strunecký, Bohunická, J.R.Johansen & J.Komárek, 2017
• Anagnostidinema amphibium (C.Agardh ex Gomont) Strunecký, Bohunická, J.R.Johansen & J.Komárek, 2017
• Anagnostidinema ionicum (Skuja) Strunecky et al., 2017
• Anagnostidinema lemmermannii (Wołoszyńska) Strunecky, Bohunická, J.R.Johansen, Capková, Raabová, P.Dvořák & Komárek, 2017
• Anathece bachmannii (Komárek & Cronberg) Komárek, Kastovsky & Jezberová, 2011
• Anathece clathrata (West & G.S.West) Komárek, Kastovsky & Jezberová, 2011
• Anathece endophytica (W. & G.S. West) Komárek, Kastovsky & Jezberová, 2011
• Anathece minutissima (West) Komárek, Kastovsky & Jezberová, 2011
• Anathece smithii (Komárková-Legnerová & Cronberg) Komárek, Kastovsky & Jezberová, 2011
• Aphanizomenon favaloroi S.H.Otaño, 2012
• Aphanizomenon flos-aquae Ralfs ex Bornet & Flahault, 1886
• Aphanizomenon gracile Lemmermann, 1907
• Aphanizomenon hungaricum Komárková-Legnerová & Mátyás, 1995
• Aphanizomenon issatschenkoi (Usachev) Proshkina-Lavrenko, 1968 accepted as Cuspidothrix issatschenkoi (Usachev) P.Rajaniemi, Komárek, R.Willame, P. Hrouzek, K.Kastovská, L.Hoffmann & K.Sivonen, 2005
• Aphanizomenon yezoense M.Watanabe, 1991
• Aphanocapsa biformis A.Braun, 1879
• Aphanocapsa conferta (West & G.S.West) Komárková-Legnerová & Cronberg, 1994
• Aphanocapsa delicatissima West & G.S.West, 1912
• Aphanocapsa elachista West & G.S.West, 1894
• Aphanocapsa fuscolutea Hansgirg, 1893
• Aphanocapsa grevillei (Berkeley) Rabenhorst, 1865
• Aphanocapsa holsatica (Lemmermann) G.Cronberg & Komárek, 1994
• Aphanocapsa incerta (Lemmermann) G.Cronberg & Komárek, 1994
• Aphanocapsa litoralis Hansgirg, 1892
• Aphanocapsa marina Hansgirg, 1890
• Aphanocapsa muscicola (Meneghini) Wille, 1919
• Aphanocapsa parasitica (Kützing) Komárek & Anagnostidis, 1995
• Aphanocapsa parietina Nägeli, 1849
• Aphanocapsa planctonica (G.M.Smith) Komárek & Anagnostidis, 1995
• Aphanocapsa raspaigellae (Hauck) Frémy, 1933
• Aphanocapsa reinboldii (Richter) Komárek & Anagnostidis, 1995
• Aphanocapsa rivularis (Carmichael) Rabenhorst, 1865
• Aphanocapsa salina Woronichin [Voronichin], 1929
• Aphanocapsa sesciacensis Frémy, 1928 (uncertain)
• Aphanocapsa stagnalis (Lemmermann) Beljakova, 2004
• Aphanocapsa thermalis Brügger, 1863
• Aphanothece bachmannii Komárková-Legnerová & G.Cronberg, 1994 accepted as Anathece bachmannii (Komárek & Cronberg) Komárek, Kastovsky & Jezberová, 2011
• Aphanothece castagnei (Kützing) Rabenhorst, 1865
• Aphanothece clathrata West & G.S.West, 1906 accepted as Anathece clathrata (West & G.S.West) Komárek, Kastovsky & Jezberová, 2011
• Aphanothece elabens (Meneghini) Elenkin, 1936
• Aphanothece marina (Ercegovic) Komárek & Anagnostidis, 1995
• Aphanothece microscopica Nägeli, 1849
• Aphanothece microspora (Meneghini) Rabenhorst, 1863
• Aphanothece minutissima (West) J.Komárková-Legnerová & G.Cronberg, 1994 accepted as Anathece minutissima (West) Komárek, Kastovsky & Jezberová, 2011
• Aphanothece nidulans P.Richter, 1884
• Aphanothece pallida (Kützing) Rabenhorst, 1863
• Aphanothece parallelliformis Cronberg, 2003
• Aphanothece saxicola Nägeli, 1849
• Aphanothece smithii Komárková-Legnerová & G.Cronberg, 1994 accepted as Anathece smithii (Komárková-Legnerová & Cronberg) Komárek, Kastovsky & Jezberová, 2011
• Aphanothece stagnina (Sprengel) A.Braun, 1863
• Arthrospira fusiformis (Voronichin) Komárek & J.W.G.Lund, 1990 accepted as Limnospira fusiformis (Voronichin) Nowicka-Krawczyk, Mühlsteinová & Hauer, 2019
• Arthrospira jenneri Stizenberger ex Gomont, 1892
• Arthrospira platensis Gomont, 1892
• Asterocapsa aerophytica F.Lederer, 2000
• Asterocapsa divina Komárek, 1993
• Asterocapsa sinica S.Y.Liang & S.G.Chen, 1985
• Beggiatoa alba (Vaucher) Trevisan, 1845
• Beggiatoa leptomitiformis Trevisan, 1842 accepted as Oscillatoria leptomitiformis Meneghini ex Gomont, 1892
• Beggiatoa mirabilis Cohn, 1865 accepted as Havrella mirabilis (Cohn) G.Breton & P.Saulot, 1986
• Blennothrix brebissonii (Kützing ex Gomont) Anagnostidis & Komárek, 1988
• Blennothrix glutinosa (Gomont) Anagnostidis & Komárek, 2001
• Blennothrix heterotricha (Gomont) Anagnostidis & Komárek, 1988
• Blennothrix lyngbyacea (Kützing ex Gomont) Anagnostidis & Komárek, 1988
• Borzia periklei Anagnostidis, 1988
• Borzia starkii J.Schiller, 1954