In this study, skin ulcer syndrome (SUS) broke out in three cage culture areas of Apostichopus japonicus in Xiaoleijiang, Wenqi and Weijiangcounty of Fujian Province in November 2023. The study analyzed the pathogenesis, bacterial structure, and correlations between bacterial and environmental factors, based on high-throughput sequencing of the 16S rDNA V3‒V4 variable region of microorganisms from sampled tissues of A. japonicus diagnosed with SUS and surrounding water samples. The bacterial community structure analysis results showed that the detected bacteria belonged to 33 phyla, 72 classes, and 350 families. The top three dominant phyla were Proteobacteria, Bacteroidota, and Actinobacteriota. The dominant bacterial families included Flavobacteriaceae, Rhodobacteraceae, Enterobacteriaceae, and Microbacteriaceae, etc. In the water samples, Proteobacteria and Bacteroidota were the two dominant phyla, and the dominant bacterial families consisted of Flavobacteriaceae, Erythrobacteriaceae, Actinomarinaceae, and unclassified Cyanobacteria. Alpha diversity analysis showed that Chao1 and ACE indices exhibited significant differences between the body wall and water samples of A. japonicus from different regions. PCoA analysis indicated that water samples clustered together, surrounding the body wall samples, suggesting that the water bacterial was associated with the health of sea cucumbers. Correlation analysis of the top 20 microflora at the family level in the diseased tissue and water samples revealed that 100 pairs of 18 microflora had significant correlations, with the correlation coefficients between Trichospirillaceae, Spirillaceae, and Muribaculaceae exceeding 0.95. Correlation analysis between microbial flora and environmental factors indicated that environmental factors BOD/Hg/Zn/Ni were significantly correlated with microbial alpha diversity (P＜0.05) of diseased tissues and water samples. The results above indicated that the diseased tissues had certain association with the flora in the water, and the environmental factors had considerable effects on the structure of the flora and the stability of the microecology. This study provided some scientific basis for the prevention and control of A. japonicus skin ulcer syndrome, while supporting the preservation of culture environment and the optimization of the culture process for sea cucumber.