This study aimed to understand the bacterial diversity of wild carp in the Eerqisi River， Xinjiang， China. The V4 region of the 16S rRNA gene were analyzed by high-throughput sequencing to compare the bacterial community composition and diversity in the intestine of carp. Results showed that a total of 35289 effective sequences and 158 OTUs were obtained. Diversity analysis indicated that the Shannon index in hindgut of carp was lowest and bacterial community structure was the most complex； the Shannon and Simpson index of foregut was more close to that of midgut. At the phylum level， Firmicutes， Proteobacteria， Bacteroidetes and Actinobacteria dominated the microbiota of carp intestine， Proteobacteria was the most dominant in foregut and midgut. However， Proteobacteria was decreased significantly with increasing in hindgut， Firmicutes was increased sharply. On the genus level， Carnobacterium is the most abundant one in hingut， the proportion of its own sequences reached 30.52%. Acidithiobacillus was the main bacterial populations in foregut and midgut. Difference were observed the bacterial community composition and diversity in different sections of the carp intestine， and the bacterial community composition in foregut and midgut were relatively similar， there was no significant difference.