The intestinal flora of fishes has attracted considerable attention in recent years; however, most scholars focus their attention on farmed fish rather than wild coral reef fish. Here, we collected gill and intestinal samples of Gnathodentex aurolineatus from three reefs in the South China Sea to compare the structures of their intestinal bacterial community and carbon source utilization characteristics. MiSeq high-throughput sequencing technology was used to investigate the intestinal bacterial community structure of G. aurolineatus and the Biolog Eco microplate method was used to analyze the carbon source utilization characteristics of bacterial communities in different reef waters. The results showed that the gill tissue and intestinal bacterial communities were highly similar across various seas. Nevertheless, significant differences in relative abundance of phyla and genera were observed. A total of 151 common operational taxonomic units (OTUs) were observed among all samples, and a total of 1022 OTUs were identified from the Yongshu Reef group. A total of 492 OTUs were identified from the Chenhang Island group. At the phylum level, Proteobacteria, Bacteroidetes, and Firmicutes were the dominant phyla in all groups, and the unique dominant phyla were Actinobacteria and Fusobacteria. At the genus level, Escherichia-Shigella, Bacteroides, Bifidobacterium, Phascolarctobacterium, Photobacterium, Marispirillum, and Pandoraea dominated in all gill tissue samples. However, the most common dominant genera were Escherichia-Shigella and Bacteroides in all intestinal samples, and other dominant genera were significantly dissimilar. Metabolic activity and utilization rate of carbon sources of amino acids, carbohydrates, and lipids ranged from high to low in Zhubi Reef group (ZB), Yongshu Reef group (YS), and Chenhang Island group (CH), with significant differences among the three groups (P＜0.05). Gene functional prediction results showed a high proportion of metabolism-related functional genes, and the utilization of the three types of carbon sources was consistent with that of carbon sources in culturable intestinal bacteria. The intestinal bacterial community of G. aurolineatus has a high metabolic capacity for carbon sources. Therefore, we plan to isolate high enzymeproducing strains from the intestines of this species in the future.