To explore the dynamics of microflora on diseased and healthy skin or in water samples of Andrias davidianus in natural environment, and provide microbial basis for rational aquaculture, protection of wild A. davidianus and future development of probiotics to improve the breeding of A. davidianus, in this study, the skin microflora of A. davidianus were profiled by high-throughput sequencing of the V4-V5 region of 16S rDNA gene, and the changes of skin microflora were compared between the healthy and the diseased A. davidianus. There were significant differences in the diversity, structure and function between healthy and diseased A. davidianus skin bacteria.The average number of Tag of each sample was 97 150, and the average length of sequencing was 400 bp. The OTU data showed that the microbial abundance of healthy skin was much higher than that of diseased skin. The dominant bacterium in the living water samples of healthy A. davidianus was Aliihoeflea, and after A. davidianus died, it changed to Chryseobacterium. The abundance of Chryseobacterium, Comamonas and Burkholderiales increased significantly, while that of Aliihoeflea, Exiguobacterium and Planococcus rifietoensis decreased significantly (P<0.05). Meanwhile, the skin surface of the dead Andrias davidianus had a large number of ulcers with pili, with typical symptoms of Burkella infection. Our findings confirmed that there were significant differences in skin microflora of dead and diseased A. davidianus. Burkella zoonotic bacteria might be the main cause of the death of A. davidianus in natural environment contaminated by water vector. This provided a basis for scientific breeding of A. davidianus.