| Protoperidinium digitale C.H.G. Pouchet, 1883 |
| Protoperidinium divaricatum (Meunier) Balech, 1976 |
| Protoperidinium divergens (Ehrenb.) Balech, 1974 |
| Protoperidinium elegans (Cleve) Balech, 1974 |
| Protoperidinium elegans f. granulatum (Karsten) Matzen., 1933 |
| Protoperidinium excentricum (Paulsen) Balech, 1974 |
| Protoperidinium fastum Balech, 1979 |
| Protoperidinium fatulipes (Kof.) Balech, 1974 |
| Protoperidinium gaarderae (Balech) Balech, 1974 |
| Protoperidinium globulum (F. Stein) Balech, 1974 |
| Protoperidinium grande (Kof.) Balech, 1974 |
| Protoperidinium granii (Ostenf.) Balech, 1974 |
| Protoperidinium hamatum Balech, 1974 |
| Protoperidinium heteracanthum (P.A. Dang.) Balech, 1974 |
| Protoperidinium hirobis (T.H. Abé) Balech, 1974 |
| Protoperidinium inclinatum (Balech) Balech, 1974 |
| Protoperidinium incognitum (Balech) Balech, 1974 |
| Protoperidinium inflatum (Okamura) Balech, 1974 |
| Protoperidinium joergenseni (Balech) Balech, 1974 |
| Protoperidinium joergenseni var. luculentum Balech, 1988 |