Some dinoflagellates are known to parasitize marine organisms, such as protists (including other dinoflagellates), copepods, chaetognaths, appendicularians and crustacean decapods and they can potentially have serious negative impacts on these host organisms. In this paper, we reviewed the present status of taxonomic studies on parasitic dinoflagellates occurring in Japanese coastal waters. We also briefly reviewed our recent knowledge on the molecular phylogenetics of parasitic dinoflagellates. So far, members of the genera, Blastodinium, Oodinium, Dissodinium, Syndinium, Amoebophrya and Duboscquella have been reported from various parts of Japan and their morphology, as well as their phylogenetic affinities, were investigated. Since our knowledge on these dinoflagellates is still limited, biodiversity studies on these organisms are a research priority.