A heterotrophic dinoflagellate was identified as Diplopsalis caspica Ostenfeld by morphological characteristics, with the plate formula: Po, x, 3′, 1a, 6″, 4c, 4s, 5″′, 1″″. The newly recorded dinoflagellate was encountered during autumn in the phytoplankton community of Jihongtan Reservoir and some small ponds near the reservoir in Shandong Province, China. The species had been reported only in brackish ecosystems; however, our material fit with D. caspica occurred in freshwater habitat. The phylogenetic relationship of D. caspica was elucidated through small and large subunit ribosomal DNA sequences. In small and large subunit ribosomal DNA phylogenies, all Protoperidiniaceae species, including diplopsalids and Protoperidinium Bergh, could cluster into a monophyletic group. The molecular phylogenies indicated that the genus Diplopsalis would provide a link to the common ancestor of the Peridinium Ehrenberg and the Protoperidinium.