| Cyclotella litoralis Lange & Syvertsen, 1989 |
| Cyclotella meneghiniana Kütz., 1844 |
| Cyclotella ocellata Pant., 1901 |
| Cyclotella operculata (C. Agardh) Bréb., 1838 |
| Cyclotella planctonica Brunnthaler, 1901 |
| Cyclotella plitvicensis Hust., 1945 |
| Cyclotella poyeka D. Avendaño & M. Caballero, 2022 |
| Cyclotella pseudostelligera Hustedt, 1939 |
| Cyclotella quillensis Bailey, 1924 |
| Cyclotella regina Mann, 1907 |
| Cyclotella rossii Håk., 1990 |
| Cyclotella stelligera (Cleve & Grunow) Van Heurck, 1882 |
| Cyclotella striata (Kütz.) Grunow, 1880 |
| Cyclotella striata var. ambigua (Grunow) Grunow, 1882 |
| Cyclotella striata var. bipunctata Fricke, 1900 |
| Cyclotella striata var. striata (Kütz.) Grunow, 1880 |
| Cyclotella stylorum Brightw., 1860 |
| Cyclotella tlalocii D. Avendaño & M. Caballero, 2022 |
| Cymatotheca N.I. Hendey, 1958 |
| Cymatotheca minima M. Voigt, 1960 |