• Agmenellum quadruplicatum (Meneghini) Brébisson, 1839 accepted as Merismopedia quadruplicata (Meneghini) Trevisan, 1845
• 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 parallelliformis Cronberg, 2003
• 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) Belyakova, 2004
• Aphanocapsa stagnalis (Lemmermann) Joosten, 2006 accepted as Aphanocapsa stagnalis (Lemmermann) Belyakova, 2004
• Aphanocapsa thermalis Brügger, 1863
• Eucapsis alpina F.E.Clements & H.L.Schantz, 1909
• Eucapsis aphanocapsoides (Skuja) Komárek & Hindák, 2016
• Eucapsis microscopica (Komárková-Legnerová & G.Cronberg) Komárek & Hindák, 2016
• Eucapsis minor (Skuja) Elenkin, 1933
• Eucapsis minuta F.E.Fritsch, 1912
• Holopedium dietelii (Richter) Migula, 1905 accepted as Microcrocis geminata (Lagerheim) Geitler, 1942
• Merismopedia elegans A.Braun ex Kützing, 1849
• Merismopedia glauca (Ehrenberg) Kützing, 1845
• Merismopedia glauca f. mediterranea (Nägeli) Collins, 1910 accepted as Merismopedia mediterranea Nägeli, 1849
• Merismopedia mediterranea Nägeli, 1849
• Merismopedia minima G.Beck, 1897
• Merismopedia punctata Meyen, 1839 accepted as Merismopedia tranquilla (Ehrenberg) Trevisan, 1845
• Merismopedia quadruplicata (Meneghini) Trevisan, 1845
• Merismopedia smithii de Toni, 1939
• Merismopedia tenuissima Lemmermann, 1898
• Merismopedia tranquilla (Ehrenberg) Trevisan, 1845
• Merismopedia trolleri Bachmann, 1920
• Merismopedia warmingiana (Lagerheim) Forti, 1907
• Synechocystis aquatilis Sauvageau, 1892
• Synechocystis crassa Woronichin, 1929
• Synechocystis diplococca (Pringsheim) Bourrelly, 1970
• Synechocystis endobiotica (Elenkin & Hollerbach) Elenkin, 1938
• Synechocystis minuscula Woronichin, 1926
• Synechocystis pevalekii Ercegovic, 1925
• Synechocystis salina Wislouch, 1924
• Synechocystis sallensis Skuja, 1930
• Synechocystis thermalis J.J.Copeland, 1936