Abstract: The microbial species in Qintong fish balls stored at 4 ℃ were analyzed by high throughput sequencing and traditional pure culture method, and the change of microbial flora in Qintong fish balls during low temperature storage was investigated. The results showed that in the initial community composition analysis of Qintong fish balls, 21 phylum, 39 classes, 49 orders, 49 families and 52 genera were found. At genus level, Pseudomonas was the dominant genus, accounting for 15%. In the late storage stage, both Pseudomonas and Psychrobacter had larger abundance. Both high throughput sequencing and traditional pure culture results showed that Pseudomonas was the dominant bacteria for fish ball spoilage, but the proportion varied.