Gut microbiota is now known to influence a range of health related aspects of fish. But how different the microbial community is in closely related fish species, and if these differences can be interpreted as adaptive is still unclear. Understanding the composition of these microbial communities is essential to health management, and the application to commercially valuable freshwater fish still requires basic investigation. The microbial communities in gut content samples and gut mucosa samples collected from the Wuchang bream (Megalobrama amblycephala) and silver carp (Hypophthalmichthys molitrix), both cohabiting in the same pond, were investigated using barcoded pyrosequencing. The specimens of the two species were cohabiting in the same pond. A total of 72,476 effective sequences were obtained from eight gut samples. These sequences were, which clustered into a total of 2528 OTUs at the 97% similarity level. It was found that there was higher microbial diversity in the gut of filter-feeding silver carp than in the gut of wuchang bream, a grazing feeding species. Fusobacteria, Proteobacteria, Firmicutes and Bacteroidetes, were detected as the predominant bacterial phyla regardless of fish or gut typeniches. At the genus level, the overwhelming group was Cetobacterium (86.56?6.63%) in Wuchang bream, while its abundance averaged c. 19% of the sequences in silver carp. Weighted UniFrac distance-based Principal Coordinates Analysis (PCoA) and the heatmap analysis showed that the gut microbiota of silver carp and Wuchang bream were clearly separated into two clusters. The microbial community structures in the intestinal contents of the two species were significantly different, but it was not true for the mucosa bacterial profiles of the two species were not. Furthermore, unique and shared OTUs in each gut type were identified. Among the 37 phylotypes which were discovered as high-dimensional biomarkers for separating shared intestinal contents microbiota between wuchang bream and silver carp, two OTUs (Otu00001 and Otu00003) from the genus Cetobacterium were found significantly more abundant in wuchang bream samples, and the remaining, such as OTU-00030 (genus Rhodopirellula), OTU-00017 (genus Proteocatella), OTU-00013 (genus Steroidobacter), etc. , had higher abundances in silver carp. These differences were presumably caused by the differences in the type of feeding habits, the physiological behavior, immune and metabolic characteristics between Wuchang bream and silver carp.