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The benthic dinoflagellate Prorocentrum lima has a cosmopolitan distribution that extends from temperate to tropical oceans. The identification of P. lima needs detailed morphological observation and molecular characterization because of its similarity to congeners and its morphological variation. In this study, we characterized different morphotypes of P. lima found in six sampling sites from Hainan Island, South China Sea, associated with macroalgae and seagrass. Twenty strains were isolated and cultivated, and P. lima was characterized using light and scanning electron microscopy in combination with large-subunit (LSU) and internal transcribed spacer (ITS) rDNA phylogeny. High morphological variability and genetic divergence was observed. Molecular analysis based on LSU and ITS rDNA sequences clearly indicated that the different morphotypes of P. lima were genetically based. The morphological and molecular data determined here suggest that all five morphotypes of P. lima examined from Hainan ...