[Background] In June 2016, Takifugu bimaculatus, cultured in Fujian Seawater Fish Seedling Breeding Research Base, outbroke the skin ulceration disease. The main symptoms of diseased fishes were characterized by slow swimming, lack of appetite, ulceration of mouth, epidermis and fins, and severe hyperemia of kidneys and spleen. [Objective] Identify the pathogenic, and provide the technical support for effectively preventing and treating skin ulceration in T. bimaculatus farming. [Methods] The dominant strains were isolated from the kidney, spleen and muscle tissue of diseased fish. The strains were confirmed to be a pathogenic bacterium by artificial intramuscular injection. The strains were identified by morphological, physiological and biochemical characteristics analysis, 16S rRNA gene sequence analysis, phylogenetic tree construction, and drug sensitivity analysis. [Results] The dominant strain SBDFT-1# was isolated from spleen of diseased fish, and was confirmed to be pathogenic strain of the skin ulceration disease. Strain SBDFT-1# was identified as Vibrio harveyi, with the morphological indexes of Gram-negative, single-flagellate, short rod-shaped, and a cell size of 0.9×2.0 μm. The colony of strain SBDFT-1# was milky white and yellow on the 2216E and TCBS plate medium, respectively, which were both central bulge and neat-transparent edges. Strain SBDFT-1# was sensitive to 14 antibiotics including Oxacillin, Cefotaxime, Ofloxacin, Streptomycin, Co-trimoxazole and Polymyxin B; while strain SBDFT-1# was resistant to 9 antibiotics such as Ampicillin, Penicillin, Tetracycline and Medecamycin. [Conclusion] This is the first report of V. harveyi as a pathogenic strain, isolated from the diseased T. bimaculatus, while it is a common pathogen in the economical fish farming. The study has a positive significantly guiding for the prevention and treatment of skin ulceration of T. bimaculatus.