| Protoperidinium cassum (Balech) Balech, 1974 |
| Protoperidinium cassum var. descens (Balech) Balech, 1988 |
| Protoperidinium cepa (Balech) Balech, 1974 |
| Protoperidinium cerasus (Paulsen) Balech, 1973 |
| Protoperidinium claudicans (Paulsen) Balech, 1974 |
| Protoperidinium compressum (T.H. Abé) Balech, 1974 |
| Protoperidinium conicoides (Paulsen) Balech, 1973 |
| Protoperidinium conicum (Gran) Balech, 1974 |
| Protoperidinium corniculum (Kof. & J.R. Michener) F.J.R. Taylor & Balech, 1979 |
| Protoperidinium crassipes (Kof.) Balech, 1974 |
| Protoperidinium cruciferum (Balech) Balech, 1973 |
| Protoperidinium curtipes (Jørg.) Balech, 1974 |
| Protoperidinium curtipes f. asymmetricum (Matzen.) Okolodkov, 2006 |
| Protoperidinium curvipes (Ostenf.) Balech, 1974 |
| Protoperidinium dakariense (P.A. Dang.) Balech, 1974 |
| Protoperidinium decipiens (Jørg.) Parke & J.D. Dodge, 1976 |
| Protoperidinium denticulatum (Gran & Braarud) Balech, 1974 |
| Protoperidinium depressum (Bailey) Balech, 1974 |
| Protoperidinium depressum var. claudicanoides (H.W. Graham) F.J.R. Taylor |
| Protoperidinium diabolus (Cleve) Balech, 1974 |