Morphological and genetic diversity of marine armored dinoflagellates in the Amphidomataceae is important for early detection of azaspiracid (AZA) producing species for seafood safety. AZAs have so far been detected from four amphidomatacean dinoflagellates, Azadinium dexteroporum, Az. poporum, Az. spinosum, and Amphidoma languida. In this study, species diversity of Azadinium and Amphidoma belonging to the family was examined by using culture strains and environmental DNA (eDNA) obtained from Japanese coastal and offshore waters since 2016. Based on the morphology and phylogeny of culture strains, 12 species including four newly described species Azadinium anteroporum, Az. fusiforme, Az. inconspicuum, and Amphidoma fulgenswere found in Japanese waters. Among 81 cultures examined, 47 cultures were assigned to Az. poporum that belonged to four intraspecific ribotypes. Based on eDNA (ITS2) metabarcoding off the Pacific coast of Hokkaido, Japan, 14 amphidomataceans were detected. Of these, Az. concinnum, Az. obesum, Az. perforatum, Az. polongum and Am. parvula were found for the first time in Japan. eDNA read numbers also showed the relatively abundant occurrences of Az. dalianense, Az. dexteroporum, Az. polongum, Az. spinosum, and Am. fulgens. These results suggest that the major AZA-producers are Az. poporum in coasts and Az. spinosum in offshore of Japanese waters.