Abstract: The occurrence of harmful algal blooms (HABs) has increased in the worldwide sea areas and poses a great threat to human health, fishery resources and marine ecosystems. Alexandrium is a major HABs genus of dinoflagellates. However, morphological differences among species of Alexandrium are very subtle under the microscopic observation. In this study, phylogenetic relationship of four Alexandrium strains collected from Southeast China were explored using D1-D2 regions of large subunit (LSU) and ITS-5.8S (internal transcribed spacer) rDNA sequences. Both the LSU and ITS rDNA sequences show that the local Alexandrium strains are closely related to each other and to the strains from Japan and Korea. Maximum likelihood phylogenetic analysis of D1-D2 regions of LSU and ITS-5.8S rDNA sequences established the four strains in a high bootstrap support clade with A. catanella/tamarense strains from East Asia. The homogeneity of rDNA sequences of the Chinese strains and East Asia strains indicates their close genetic relationship with the temperate Asian ribotype, implying that the Chinese A. catanella/tamarense complex is unlikely to have been introduced from Europe or the other sea areas other than Asia through ballast water or other vectors. Similarities in LSU and ITS-5.8S sequences indicate that A. catenella and A. tamarense are conspecifics rather than interspecifics.