• Cyclotella (F.T. Kützing) A. de Brébisson, 1838
• Cyclotella abnormis Cleve-Euler, 1915 (uncertain > unassessed)
• Cyclotella actinocyclus (Ehrenberg) Kützing, 1849 accepted as Pyxidicula actinocyclus Ehrenberg, 1844
• Cyclotella actinopleurata E. Clerici, 1907 (uncertain > unassessed)
• Cyclotella aegaea A.Economou-Amilli, 1987 (uncertain > unassessed)
• Cyclotella aegaea var. pythagorea A.Economou-Amilli, 1987 (uncertain > unassessed)
• Cyclotella affinis Grunow in Möller (uncertain > unassessed)
• Cyclotella affinis Makarova & Genkal accepted as Cyclotella caspia var. affinis Proschkina-Lavrenko & Makarova in Makarova & Proschkina-Lavrenko, 1964
• Cyclotella afrerensis Gasse, 1974 (uncertain > unassessed)
• Cyclotella africana Rabenhorst, 1855 (uncertain > unassessed)
• Cyclotella agassizensis Håkansson & Kling, 1994 (uncertain > unassessed)
• Cyclotella alchichicana Olivia, Lugo, Alocer & Cantoral-Uriza, 2006 (uncertain > unassessed)
• Cyclotella aliquantula Hohn & Hellermann, 1963 (uncertain > unassessed)
• Cyclotella ambigua Grunow, 1880 (uncertain > unassessed)
• Cyclotella americana (Ehrenberg) Kützing, 1849 accepted as Discoplea americana Ehrenberg, 1844
• Cyclotella americana Schmidt in Schmidt et al., 1900 (uncertain > unassessed)
• Cyclotella andancensis Ehrlich, 1967 accepted as Pantocsekiella andancensis (A. Ehrlich, 1967) K.T. Kiss, Ector & Ács, 2016
• Cyclotella andancensis var. bauzilensis Serieyssol, 1981 (uncertain > unassessed)
• Cyclotella andancensis var. bipolaira Serieyssol, 1981 (uncertain > unassessed)
• Cyclotella andina E.Theriot, H.J.Carney & P.J.Richerson, 1985 (uncertain > unassessed)
• Cyclotella annulata Suringar, 1870 (uncertain > unassessed)
• Cyclotella anomala K.E. Lohman, 1957 (uncertain > unassessed)
• Cyclotella antigua W.Smith, 1853 accepted as Cyclotella antiqua W.Smith, 1853 accepted as Lindavia antiqua (W.Smith) Nakov et al., 2015
• Cyclotella antiqua W.Smith, 1853 accepted as Lindavia antiqua (W.Smith) Nakov et al., 2015
• Cyclotella antiqua var. antiqua W. Smith, 1853 (uncertain > unassessed)
• Cyclotella antiqua var. labynkyrensis Komarenko in Komarenko & Vasilyeva, 1975 (uncertain > unassessed)
• Cyclotella antiqua var. minor Suxena & Venkateswarlu, 1968 (uncertain > unassessed)
• Cyclotella antiqua var. mirifica Héribaud, 1903 (uncertain > unassessed)
• Cyclotella antiqua var. vernierei Héribaud, 1903 (uncertain > unassessed)
• Cyclotella arctica Genkal & Kharitonov, 1996 accepted as Pantocsekiella arctica (Genkal & Kharitonov, 1996) K.T. Kiss, Genkal & Ács, 2016
• Cyclotella arentii Kolbe, 1948 (uncertain > unassessed)
• Cyclotella areolata Hustedt, 1935 (uncertain > unassessed)
• Cyclotella armenica Loginova & Pirumova in Loginova, Aleshinskaya & Pirumova, 1990 accepted as Lindavia armenica (Loginova & Pirumova) Nakov et al., 2015
• Cyclotella asiatica Brun in Brun & Tempère, 1889 (uncertain > unassessed)
• Cyclotella asperula Marsson, 1901 (uncertain > unassessed)
• Cyclotella asterocostata Lin, Xie & Cai, 1985 (uncertain > unassessed)
• Cyclotella asterocostata var. striata Chen, 1987 (uncertain > unassessed)
• Cyclotella asterolampra Lauby, 1910 (uncertain > unassessed)
• Cyclotella astraea Kützing, 1849 accepted as Discoplea astraea Ehrenberg, 1844 †
• Cyclotella astraea var. carconensis Eulenstein ex Grunow (uncertain > unassessed)
• Cyclotella astraea var. spinosa Schumann, 1867 (uncertain > unassessed)
• Cyclotella atlantica (Ehrenberg) Ralfs in Pritchard, 1861 accepted as Discoplea atlantica Ehrenberg, 1854
• Cyclotella atmosphaerica Ralfs accepted as Discoplea atmosphaerica Ehrenberg, 1847
• Cyclotella atomoides Marvan in Kubicek, Marvan & Zelinka, 1958 (uncertain > unassessed)
• Cyclotella atomus Hustedt, 1937 (uncertain > unassessed)
• Cyclotella atomus var. atomus Hustedt accepted as Cyclotella atomus Hustedt, 1937
• Cyclotella atomus var. gracilis Genkal & Kiss, 1993 (uncertain > unassessed)
• Cyclotella austriaca (M.Peragallo, Handmann & Schiedler) Hustedt, 1948 accepted as Handmannia austriaca f. austriaca M. Peragallo in Handmann, 1913
• Cyclotella azigzensis R.J.Flower, F.Gasse & H.Håkansson, 1990 accepted as Pantocsekiella azigzensis (Flower et al., 1990) K.T. Kiss & Ács, 2016
• Cyclotella bachmannii Meister, 1912 (uncertain > unassessed)
• Cyclotella baicalensis Skvortzov, 1927
• Cyclotella baicalensis f. baicalensis Skvortzow & Meyer, 1928 accepted as Lindavia baicalensis (Skvortzow & Meyer) Nakov et al., 2015
• Cyclotella baicalensis f. minor Skvortzow & Meyer, 1928 (uncertain > unassessed)
• Cyclotella baicalensis f. minuta Skvortzow, 1937 accepted as Lindavia minuta (Skvortzow) Nakov et al., 2015
• Cyclotella baicalensis f. ornata Skvortzow, 1937 accepted as Lindavia ornata (Skvortzow) Nakov et al., 2015
• Cyclotella baicalensis f. stellata Skvortzow, 1937 (uncertain > unassessed)
• Cyclotella baicalensis f. typica Skvortzow, 1937 (uncertain > unassessed)
• Cyclotella balatonis Pantocsek, 1901
• Cyclotella balatonis var. balatonis Pantocsek, 1902 accepted as Lindavia balatonis (Pantocsek) Nakov et al., 2015
• Cyclotella balatonis var. binotata Pantocsek, 1902 accepted as Handmannia balatonis (Pantocsek, 1902) Kulikovskiy & Solak, 2013
• Cyclotella baltica (Grunow) H.Håkansson accepted as Cyclotella striata var. baltica Grunow in Van Heurck, 1882
• Cyclotella bastowii J.R.Carter, 1961 † (uncertain > unassessed)
• Cyclotella bavarica Klee, Schmidt & Muller, 1993 accepted as Pantocsekiella bavarica (Klee, Rol. Schmidt & Jens Müller, 1993) K.T. Kiss &Ács, 2016
• Cyclotella bella Schmidt, 1874 (uncertain > unassessed)
• Cyclotella berguisensis Ehrlich, 1969 (uncertain > unassessed)
• Cyclotella bifacialis Jurilj, 1954 (uncertain > unassessed)
• Cyclotella bisymmetrica Loseva, 1983 (uncertain > unassessed)
• Cyclotella bituminosa Hustedt, 1952 (uncertain > unassessed)
• Cyclotella bodanica Eulenstein ex Grunow, 1878 accepted as Lindavia bodanica (Eulenstein ex Grunow) Nakov et al., 2015
• Cyclotella bodanica f. borealis (Cleve-Euler) Cleve-Euler, 1951 accepted as Cyclotella bodanica var. borealis Cleve-Euler, 1911
• Cyclotella bodanica f. lemanensis (O. Mull.) Skabichevskii, 1960 (uncertain > unassessed)
• Cyclotella bodanica f. lemanica (Otto Muller in Schroter; Otto Muller in Chodat) Bachmann, 1903 accepted as Lindavia lemanensis (Chodat) Nakov et al., 2015
• Cyclotella bodanica var. affinis (Grunow) A.Cleve, 1951 accepted as Cyclotella comta f. affinis Grunow in Van Heurck, 1882
• Cyclotella bodanica var. affinis Grunow, 1878 accepted as Lindavia affinis (Grunow) Nakov et al., 2015
• Cyclotella bodanica var. bodanica Eulenstein in Grunow, 1878 (uncertain > unassessed)
• Cyclotella bodanica var. borealis Cleve-Euler, 1911 (uncertain > unassessed)
• Cyclotella bodanica var. genuina Cleve-Euler, 1951 (uncertain > unassessed)
• Cyclotella bodanica var. intermedia Manguin ex Kociolek & Reviers, 1996 accepted as Lindavia intermedia (Manguin ex Kociolek & Reviers) Nakov et al., 2015
• Cyclotella bodanica var. jacutica Komarenko in Komarenko & Vasilyeva, 1975 (uncertain > unassessed)
• Cyclotella bodanica var. michiganensis Skvortzow, 1937 (uncertain > unassessed)
• Cyclotella bodanica var. nonpunctata Cleve-Euler in Backman & Cleve-Euler, 1922 (uncertain > unassessed)
• Cyclotella bodanica var. robusta Skabichevskaya, 1984 (uncertain > unassessed)
• Cyclotella bodanica var. stellata Skvortzow, 1937 (uncertain > unassessed)
• Cyclotella bomba Serieyssol, 1981 (uncertain > unassessed)
• Cyclotella calae Azpeitia, 1911 (uncertain > unassessed)
• Cyclotella californica Grunow ex Cleve & Möller, 1879 (uncertain > unassessed)
• Cyclotella cantalense (Héribaud) Mills, 1933 accepted as Cymbella cantalense Héribaud, 1908
• Cyclotella carconensis Eulenstein ms. Grunow, 1878 (uncertain > unassessed)
• Cyclotella caspia Grunow, 1878 (uncertain > unassessed)
• Cyclotella caspia var. affinis Proschkina-Lavrenko & Makarova in Makarova & Proschkina-Lavrenko, 1964 (uncertain > unassessed)
• Cyclotella caspia var. clitumnii Granetti, 1967 (uncertain > unassessed)
• Cyclotella cassandrae Paillès & Sylvestre in Paillès et al., 2018 †
• Cyclotella castracanei Eulenstein ex Fricke in Schmidt et al., 1901 (uncertain > unassessed)
• Cyclotella castracanei Eulenstein ms in Rattray, 1890 (uncertain > unassessed)
• Cyclotella castracani Brun, 1891 (uncertain > unassessed)
• Cyclotella castracaniensis Eulenstein in H.L. Smith, 1874 (uncertain > unassessed)
• Cyclotella catenata (J.Brun) Bachmann, 1911 accepted as Melosira catenata Brun, 1895
• Cyclotella cavita Stoermer & Kreis, 1978 (uncertain > unassessed)
• Cyclotella cavitata Tofilovska, Cvetkoska, Jovanovska, Ognjanova-Rumenova & Levkov, 2016 †
• Cyclotella cesatii Castracane, 1866 (uncertain > unassessed)