Abstract: Mosaic disease is a novel disease that has emerged during the culture of Chinese sturgeon (Acipenser sinensis) in recent years. In order to study the flora markers for monitoring the health status of A. sinensis, we analyzed the microbial community structure of the skin mucosa of healthy and diseased juveniles by using high-throughput sequencing technology. The results show that compared with healthy fish, the diversity and richness of diseased fish reduced significantly (p<0.001). On genus level, the skin mucosa of healthy fish was composed of Lactobacillus, Acinetobacter, norank_f-Muribaculaceae, Leuconostoc and Pseudomonas, while the skin mucosa of diseased fish was composed of Flavobacterium and Acinetobacter, and the proportion of Flavobacterium was 78.38%. The significant difference analysis shows that five sensntive taxa were screened, reflecting the health status of Chinese sturgeon. This study indicates that compared with healthy fish, mosaic disease destroyed the normal homeostasis of microbiota in skin mucosa. The dominant bacterial community changed from Lactobacillus and Acinetobacter to Flavobacterium. Therefore, Flavobacterium have been identified as a marker to monitor the pathogen of mosaic disease in A. sinensis. Its relative abundance can be utilized to evaluate the risk of disease in A. sinensis.