• 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
• Altericista lacusladogae Averina, E.Polyakova, Senetskaya & Pinevich, 2021
• Altericista variichlora Averina, E. Polyakova, Senatskaya & Pinevich, 2021
• Altericista violacea Averina, E.Polyakova, Senatskaya & Pinevich, 2021
• Anathece bachmannii (Komárek & Cronberg) Komárek, Kastovsky & Jezberová, 2011
• Anathece bacteriosa (Komárek & Komárková-Legnrová) 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
• Anathece stratus (Komárek & Cronberg) Komárek, Kastovsky & Jezberová, 2011
• Bacillosiphon coerulescens (Borzì) Molinari & Guiry, 2021
• Bacillosiphon gracilis (Komárek) Molinari & Guiry, 2021
• Bacillosiphon induratus J.J.Copeland, 1936
• Bacillosiphon thermalis (Frémy) Molinari & Guiry, 2021
• Bacillosiphon vermicularis (Molinari & Guiry) Molinari & Guiry, 2021
• Beckia bella (Beck) Elenkin, 1938 accepted as Microcrocis bella (Beck-Mannagetta) Komárek & Anagnostidis, 1995
• Beckia solea Komarenko, 1975 accepted as Microcrocis solea (Komarenko) Komárek & Anagnostidis, 1995
• Borziella coerulescens (Borzì) Molinari & Guiry, 2021 accepted as Bacillosiphon coerulescens (Borzì) Molinari & Guiry, 2021
• Borziella gracilis (Komárek) Molinari & Guiry, 2021 accepted as Bacillosiphon gracilis (Komárek) Molinari & Guiry, 2021
• Borziella indurata (J.J.Copeland) Molinari & Guiry, 2021 accepted as Bacillosiphon induratus J.J.Copeland, 1936
• Borziella thermalis (Frémy) Molinari & Guiry, 2021 accepted as Bacillosiphon thermalis (Frémy) Molinari & Guiry, 2021
• Borziella vermicularis Molinari & Guiry, 2021 accepted as Bacillosiphon vermicularis (Molinari & Guiry) Molinari & Guiry, 2021
• Campylotropium alascense Hortobágyi & D.K.Hilliard, 1965 accepted as Romeria alascensis (Hortobágyi & D.K.Hilliard) Komárek, 2001
• Coccopedia limnetica O.V.Troitzkaja [Troickaja], 1922
• Coccopedia turkestanica E.Kiseleva, 1931
• Cyanobium amethystinum (J.J.Copeland) J.Komárek, J.Kopecký & V.Cepák, 1999
• Cyanobium bacillare (Butcher) Komárek, Kopeck & Cepák, 1999
• Cyanobium diatomicola (Geitler) Komárek, Kopecký & Cepák, 1999
• Cyanobium distomicola Geitler, 1953
• Cyanobium eximium (J.J.Copeland) Komárek, Kopecký & Cepák, 1999
• Cyanobium gaarderi (Ålvik) Komárek, Kopecký & Cepák, 1999
• Cyanobium gracile Rippka & Cohen-Bazire, 1983
• Cyanobium oceanicum (W.T.Hall & G.Claus) Komárek, Kopecký & Cepák, 1999
• Cyanobium parvum (Migula) Komárek, J.Kopecký & Cepák, 1999
• Cyanobium plancticum (G.Drews, H.Prauser & D.Uhlmann) Komárek, Kopecký & Cepák, 1999
• Cyanobium roseum (J.J.Copeland) Komárek, Kopecký & Cepák, 1999
• Cyanobium rubescens (T.P.Chang) Komárek, Kopeck & Cepák, 1999
• Cyanobium virga-rosea (T.P.Chang) Komárek, Kopecký & Cepák, 1999
• Cyanobium waterburyi Komárek, 1999
• Cyanogranis basifixa Hindák, 1982
• Cyanogranis ferruginea (F.Wawrik) Hindák ex Hindák, 2006
• Cyanogranis irregularis Joosten, 2006
• Cyanogranis libera Hindák, 2002
• Cyanonephron elegans Joosten, 2006
• Cyanonephron styloides B.Hickel, 1985
• Cyanothrix anabaeniformis Kiselev, 1940
• Cyanothrix caspica Kiselev, 1940
• Cyanothrix cavanillesii Gonzalez Guerrero, 1946
• Cyanothrix fusca (W.R.Taylor) Frémy, 1935 accepted as Nodularia fusca W.R.Taylor, 1920
• Cyanothrix gardneri (Frémy) Kiselev, 1947
• Cyanothrix gardneri f. fusca (W.R.Taylor) Kisselev (uncertain)
• Cyanothrix gardneri f. longicellularis Kogan (uncertain)
• Cyanothrix gardneri f. primaria (N.L.Gardner) Kisselev accepted as Cyanothrix primaria N.L.Gardner, 1927
• Cyanothrix gardneri f. willei (N.L.Gardner) Kisselev accepted as Cyanothrix willei N.L.Gardner, 1927
• Cyanothrix primaria N.L.Gardner, 1927
• Cyanothrix willei N.L.Gardner, 1927
• Euryhalinema epiphyticum V.L.Araújo, A.S.Schnadelbach, J.M.C.Nunes & T.A.Caires, 2022
• Euryhalinema mangrovii Chakraborty & Mukherjee, 2019
• Euryhalinema palustre S.Chakraborty & J.Mukherjee, 2021
• Halomicronema excentricum Abed, Garcia-Pichel & Hernández-Mariné, 2002
• Halomicronema hongdechloris Chen, Li, Birch & Willows, 2012
• Halomicronema metazoicum C.Caroppo, P.Pagliara & P.Albertano, 2012
• Heterohormogonium schizodichotomum J.J.Copeland, 1936 accepted as Johannesbaptistia schizodichotoma (J.J.Copeland) Komárek & Anagnostidis, 1995
• Holopedium bellum Beck-Mannagetta, 1929 accepted as Microcrocis bella (Beck-Mannagetta) Komárek & Anagnostidis, 1995
• Holopedium clementei González Guerrero, 1946 (uncertain)
• Holopedium dednense Pevalek, 1925 (uncertain)
• Holopedium dietelii (Richter) Migula, 1905 accepted as Microcrocis geminata (Lagerheim) Geitler, 1942
• Holopedium geminata (Lagerheim) Lagerheim, 1893 accepted as Microcrocis geminata (Lagerheim) Geitler, 1942
• Holopedium geminatum (Lagerheim) Lagerheim, 1893 accepted as Microcrocis geminata (Lagerheim) Geitler, 1942
• Holopedium granulatum Skuja, 1948 accepted as Microcrocis granulata (Skuja) Skuja, 1966
• Holopedium irregulare (Lagerheim) Lagerheim, 1893 accepted as Microcrocis irregularis (Lagerheim) Geitler, 1942
• Holopedium mutisiana González Guerrero, 1946
• Holopedium obvolutum Tiffany, 1934 accepted as Microcrocis obvoluta (Tiffany) T.H.Frank & A.G.Landman, 1988
• Holopedium pulchellum Buell, 1938 accepted as Microcrocis pulchella (Buell) Geitler, 1942
• Holopedium sabulicola (Lagerheim) Kirchner, 1900 accepted as Microcrocis sabulicola (Lagerheim) Geitler, 1942
• Holopedium sabulicola (Lagerheim) Lagerheim, 1893 accepted as Microcrocis sabulicola (Lagerheim) Geitler, 1942
• Inactis ecalcarea Gardner, 1927 accepted as Schizothrix ecalcarea N.L.Gardner, 1927
• Inactis funalis (West & G.S. West) Forti, 1907 accepted as Schizothrix funalis West & G.S.West, 1896
• Inactis polythrix Forti, 1907 accepted as Trichocoleus polythrix (Forti) Anagnostidis, 2001
• Inactis sauteriana Grunow ex Forti, 1907 accepted as Symplocastrum sauterianum (Grunow ex Forti) Anagnostidis, 2001
• Inactis tinctoria Thuret, 1875 accepted as Schizothrix tinctoria Gomont ex Gomont, 1892
• Inactis vaginata (Gomont) Forti, 1907 accepted as Schizothrix vaginata Gomont, 1892
• Jaaginema acuiforme (Skuja) Anagnostidis & Komárek, 1988 accepted as Geitlerinema acuiforme (Skuja) Anagnostidis, 2001
• Jaaginema angustissimum (West & G.S.West) Anagnostidis & Komárek, 1988
• Jaaginema borodinii (Woronichin) Anagnostidis & Komárek, 1988
• Jaaginema calcuttense (Biswas) Anagnostidis & Komárek, 1988 accepted as Geitlerinema calcuttense (Biswas) Anagnostidis, 1989
• Jaaginema cavanillesianum (González Guerrero) Anagnostidis, 2001
• Jaaginema crassum (Woronichin) Anagnostidis, 2001
• Jaaginema earlei (Gardner) Anagnostidis & Komárek, 1988 accepted as Geitlerinema earlei (N.L.Gardner) Anagnostidis, 1989
• Jaaginema filiforme (J.Copeland) Anagnostidis, 2001
• Jaaginema geitleri (Frémy) Anagnostidis & Komárek, 1988
• Jaaginema geminatum (Schwabe ex Gomont) Anagnostidis & Komárek, 1988
• Jaaginema geminatum sulphureum (Strzeszewski) Aysel, 2005 accepted as Geitlerinema sulphureum (Strzeszewski) Anagnostidis, 2001
• Jaaginema gracile (Böcher) Anagnostidis & Komárek, 1988
• Jaaginema homogeneum (Frémy) Anagnostidis & Komárek, 1988