Sea cucumber (Apostichopus japonicus), an important economic mariculture species in China, has high nutritional and medicinal values. In recent years, with the expansion of the breeding scale, new pathogens causing diseases often appear. In November 2020, a large-scale epidemic of skin ulcers was recorded in cultured A. japonicus in the Xiapu area of Fujian Province. In order to explore the pathogens causing diseases in A. japonicus, the potentially pathogenic bacteria were isolated, and the physicochemical properties, virulence factors, and drug sensitivity of the isolated bacteria were studied. The artificial regression infection results showed that the dominant strain isolated from the lesions on the body surface (XP-11) was the main pathogen causing the skin rot syndrome in A. japonicus, with the same symptoms of skin ulcers as the natural disease. The results showed that the dominant strain XP-11 isolated from the lesions on the body surface was the main pathogen causing the skin rot syndrome in A. japonicus. The strain XP-11 was identified as Photobacterium damselae subsp. damselae based on morphological characteristics, Biolog’s automatic microbial identification system, as well as 16S rRNA, housekeeping gene (gyrB), and urease C (ureC) gene sequence analyses. The results of virulence gene detection showed that the strain XP-11 contains two typical virulence genes of the hemolysin gene (hlyAch) and phospholipase activity gene (plpV). The results of antimicrobial susceptibility analysis showed that the strain XP-11 was sensitive to tetracycline, enrofloxacin, and trimethoprim/sulfamethoxazole. The minimum inhibitory concentrations of the strain XP-11 to Enrofloxacin, Neomycin sulfate, Thiamphenicol, Florfenicol, Doxycycline hydrochloride, Flumequine, sodium Sulfamethoxine, Sulfamethoxazole + Trimethoprim were 0.08, 2, 1, 1, 0.06, 0.125, 4, and 1.2/0.06 μg/mL, respectively. This is the first report regarding the diseases caused by P. damselae in sea cucumbers. In summary, P. damselae subsp. damselae was the causative agent of the skin ulceration syndrome of cultured A. japonicus, and the median lethal dose (LD₅₀) value was 1.08×10⁵ CFU/g body weight. The results of this study provided valuable references for further prevention and control of diseases caused by P. damselae in the sea cucumber aquaculture industry.