Abstract: Three strains of Chattonella spp. were isolated from the Beibu Gulf in September 2018 and were identified using light microscopy and phylogenetic analysis based on LSU rDNA and ITS gene sequencing. Results show that the Chattonella spp. strains from the Beibu Gulf are yellowish-brown; the cells are spindle-shaped with a pointed posterior end, and mucocysts are absent; the average cell length is (57.8±9.1) μm. These characteristics are consistent with the typical morphological characteristics of C. marina. In phylogenetic trees, the strains from the Beibu Gulf were clustered with C. marina, C. antiqua, C. ovata, and C. minima, with bootstrap value of 96% and 99% for LSU rDNA and ITS, respectively. Genetic distance analysis demonstrated that the three Chattonella spp. strains in the Beibu Gulf were closely related to C. marina, C. antiqua, C. ovata, and C. minima with genetic distances of 0.0000~0.0016 and 0.0000~0.0235, while being distantly related to C. subsalsa with genetic distances of 0.0415~0.0490 and 0.0733~0.0750 for LSU rDNA and ITS, respectively. Therefore, our comprehensive morphological and molecular biology methods suggested that the three strains of Chattonella spp. in the Beibu Gulf belonged to C. marina/C. marina var. antiqua/C. marina var. ovata. This study is helpful for Chattonella collection in the Beibu Gulf and will support further ecophysiological studies.