Silvery pomfret (Pampus argenteus) is a kind of valuable economic fish species and the intestinal gas bubble accumulation is an important factor that hinders its popularization. In order to evaluate the changes of the bacterial communities in Silvery pomfret’s intestine upon gas bubble accumulation occurrence, 15 diseased fish were chosen as the diseased group and 15 healthy fish as the healthy group. The method of high-throughput sequencing of 16S rDNA gene’s V3-V4 region was used to determine diversity and composition of bacterial communities in each of these samples. The comparison results of the Alpha diversity index showed that there was no significant difference in the Simpson index and the Shannon index between these two groups (P > 0.05), but the Chao1 estimator and the ACE estimator in the diseased group are significantly lower than those of the healthy group (P < 0.05) (Table 1). The analysis of the microbiota structure showed that the dominant bacterial groups were similar in the diseased and control groups, at the phylum level being Proteobacteria, and at the genus level being Sphingobium, Sphingomonas, Cupriavidus, Novo sphingobium and Acinetobacter (Table 2). From the above results, it can be concluded that the intestinal gas bubble accumulation reduces the richness and evenness of intestinal flora of Silvery pomfret, but does not affect its diversity. In addition, the two groups of samples were analyzed by LEfSe and the results showed that the relative abundance of aerobic bacteria such as agrobacterium bacteria, thermophilic bacteria, cyanobacteria, rhizobial bacteria in the diseased group was significantly higher than that of the healthy group, while the relative abundance of acinetobacter and microacidic bacteria was significantly lower than that of the healthy group (Fig. 3 and Fig. 4 ). From these results, it can be concluded that the intestinal gas bubble accumulation may cause intestinal flora disorder.