To explore the relationship between the microbial community structure of the skin mucosa of Chinese sturgeons and plate discoloration disease, this study analyzed the structural characteristics of the microbial communities of the dorsal plate and trunk skins of healthy and diseased Chinese sturgeons using Illumina high-throughput sequencing. A total of 3406 operational taxonomic units (OTUs) were identified in the skin mucosa from the four sources. Compared to Chinese sturgeons in the healthy group, the number of OTUs in the dorsal plate skin in the disease group decreased by 84%, and that in the trunk skin decreased by 55%. At the phylum level, the composition of the dominant bacteria in the dorsal plate and trunk skins of Chinese sturgeons in the healthy group was relatively similar, with Proteobacteria, Firmicutes, and Bacteroidetes being the main bacteria, accounting for more than 75%. Bacteroidetes were highly enriched in the dorsal plate and trunk skins of the disease group; the relative abundance of the former increased from 11.15% to 67.99%, and the relative abundance of the latter increased from 20.28% to 53.48%. At the genus level, the relative abundances of Flavobacterium in the dorsal plate and trunk skins of the disease group were 42.83% and 21.78%, respectively, which were higher than that of the healthy group (4.20% and 16.92%, respectively). The relative abundances of Chryseobacterium in the dorsal plate and trunk skins of the disease group were 23.34% and 27.65%, respectively, which were higher than that of the healthy group (0.33% and 2.16%, respectively). Diversity analysis showed significant differences in the Chao and Shannon indices between the skin mucosa of Chinese sturgeons in the healthy and diseased groups (P＜0.01). The significant difference analysis showed that Flavobacterium Chryseobacterium, Acidovorax and Hydrogenophaga were significantly upregulated in the disease group (P＜0.05). This study showed that compared with the healthy Chinese sturgeon group, the number of OTUs in the dorsal plate and trunk skins of the diseased Chinese sturgeon group as well as the richness and diversity were significantly reduced (P＜0.01). Flavobacterium and Chryseobacterium of Bacteroidota were highly enriched in the skin mucosa of Chinese sturgeons in the disease group, and may be the main pathogenic bacteria of this disease.