Abstract: Focusing on the abundant fishery resources in the South China Sea, we analyzed the distribution characteristics of the microbial community in the gill tissue of bony fishes in the adjacent South China Sea by using 16S amplicon sequencing technology. In addition, we discussed the differences in the bacterial community structure at different sites. The results show that the sequencing obtained a total of 2 952 366 effective spliced fragments (Clean tags) with an average of 56 776 in each library. The dominant taxa were analyzed at phylum and genus levels. Proteobacteria was the highest (71.3%) at phylum level, and Acinetobacter was the highest at genus level (17.2%). The alpha diversity of different sites was significantly different, and the I9 and H8 sites had the highest species richness (Chao1 index), and the D3 site had the highest diversity (Shannon index). The beta diversity of samples from different sites was significantly different (P<0.05), but there was no significant difference between the host classification (Order level) groups (P>0.05). The composition of bacterial communities in the gill tissues of bony fishes in the South China Sea was abundant. Compared with the classification of the host, the sampling station has more important influence on the community of the bacterial in the gill tissues, and may play an active role in assisting the host's nutrient transport and metabolism.