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Marine benthic dinoflagellates in the genus Coolia were reported in both tropical and temperate regions. We conducted a morphological and phylogenetic characterization of Coolia species from Hainan Island, South China Sea. The morphologies of three Coolia species were similar to those of the original descriptions of Coolia canariensis , C . tropicalis , and C . malayensis . In phylogenetic analyses based on the LSU rDNA and ITS regions (ITS1-5.8S-ITS2), the Hainan strains of C . canariensis , C . tropicalis , and C . malayensis clustered within the clades of these species with other isolates from different areas. No differences (p-distance) in LSU rDNA sequences were found between the Hainan C . malayensis strains and the strains from New Zealand, Florida of USA, Malaysia, Japan, Dominican Republic and Guangxi and Hong Kong of China. For C . canariensis and C . tropicalis , no differences (p-distance) in the LSU rDNA sequences were found between the Hainan strains (D1C2 and DS5F4, respectively) and the Australian strains (NQAIF252 and NQAIF90, respectively). Our study reveals the morphological and genetic diversity of Coolia species from Hainan Island, South China Sea, which provides a detailed understanding of Coolia species of this area.