Abstract: To investigate the intestinal bacterial communities differences between the transgenic common carp and controls, carp intestinal bacterial community at different developmental stages (6 day, 2 month, 5 month) were used for 454 high throughput sequencing. Detrended correspondence analysis (DCA) showed that the intestinal bacterial communities of transgenic common carp and controls at 2 month age were significantly different. Alpha diversity and evenness results indicated that gut microbial diversity of transgenic common carp was higher than that of the control. We found that transgenic carp gut had more bacteria belonging to Firmicutes, and the controls had more bacteria belonging Bacteroidetes. The Bacteroidetes/Firmicutes ratio of transgenic common carp was significantly lower than that of controls in 2 month age. All data showed that transgenic common carp had different intestinal bacterial composition compared with wild controls at three developmental stages, especially at 2 month stage. Our findings provide insight into the interaction and mechanism between microbes and the host.