The number of cingular plates has been used to differentiate Protoperidinium from Peridinium and related genera. Protoperidinium is characterized by the presence of three cingular plates plus a transitional plate (3C+t). However, many Protoperidinium species have been described that exhibit different cingular plate tabulations. How these species should be classified within the genus remains unclear. To address this question, the phylogenetic relationship of four Protoperidinium species, with three or four cingular plates and lacking a transitional plate, were examined in relationship to other Protoperidinium species. These four species were germinated from cysts deposited in surface sediments collected from the East China Sea, the Bohai Sea and the Yellow Sea. Three of the isolated species, P. tricingulatum, P. americanum and P. parthenopes, were described previously. The fourth is here described as P. haizhouense sp. nov. with the plate formula Po, X, 4′, 3a, 7′′, 3C, 6S, 5′′′, 2′′′′. Differences in the cyst stages of these four species, which can be taxonomically informative, were compared. Partial large subunit ribosomal DNA sequences were obtained by single-cell polymerase chain reaction. Maximum-likelihood and Bayesian inference showed that these four species, P. fukuyoi and Islandinium minutum form a monophyletic clade with maximal support. The genus as a whole, however, appeared polyphyletic. Our results suggest that the presence/absence of a transitional plate is significant in the phylogeny of Protoperidinium.