Gut microbiota is increasingly regarded as an integral component of the host, due to important roles in the modulation of the immune system, the proliferation of the intestinal epithelium, and the regulation of the dietary energy intake. Understanding the factors that influence the composition of these microbial communities is essential to health management, and the application to aquatic animals still requires basic investigation. In this study, we compared the bacterial communities harboured in the intestine and in the rearing water of Grass carp (Ctenopharyngodon idellus), crucian carp (Carassius cuvieri), and bighead carp (Hypophthalmichthys nobilis), by using 454-pyrosequencing with barcoded primers targeting the V4 to V5 region of the bacterial 16S rRNA gene. The specimens of the three species were cohabiting in the same pond. Between 7,848 and 11,948 effective sequences were read from each sample, resulting in a total of 142,893 sequences for 13 samples from gut microbiota of three carps and pond water. In general, the microbial communities of the three species of fishes were all dominated by phyla Fusobacteria, Firmicutes, Bacteroidetes, and Proteobacteria, but the abundances of each phylum were significantly different from each other. At the genus level, the most abundant genera in grass carp were Cetobacterium, Bacteroides, Aeromonas, Clostridium XlVa and XlVb, but in crucian carp, the overwhelming group was Cetobacterium (96.55?0.91%), followed by Aeromonas, Bacteroides and Clostridium sensu stricto. In bighead carp, the predominant populations were Cetobacterium, Paludibacter, Clostridium sensu stricto, Clostridium XI and Proteocatella. There was higher microbial diversity in the gut of filter-feeding bighead carp than the two other grazing species. The composition of intestine microbiota of grass carp and crucian carp shared higher similarity when compared with bighead carp. The Principal Coordinates Analysis (PCoA) with the weighted UniFrac distance, and the heatmap analysis suggested that gut microbiota was not a simple reflection of the microbial community in the local habitat, but resulted from species-specific selective pressures, possibly dependent on species-specific behavioural, immune and metabolic characteristics.