To elucidate the influence of different diet on the intestinal microbe and bile acids, we characterized the microbiota and bile acids in the hindgut content of grass carp fed on formula feed (FF group) or Sudan grass (SG group). Fusobacteria and Proteobacteria were significantly more represented in FF group than in SG group whereas Bacteroidetes was significantly more abundant in SG group than in FF group. Simpson diversity was significantly higher in FF group than in SG group (t=2.33, P<0.05). Chenodeoxycholic acid (CDCA) was the most abundant primary bile acid in the two groups, with average concentrations of 1.03 +/- 0.62 and 4.44 +/- 1.80ngmg(-1) in SG and FF group respectively. The most abundant secondary bile acid was deoxycholic acid (DCA) inSG group and ursodeoxycholic acid (UDCA) in FF group, with average concentrations of 0.17 +/- 0.06 and 2.67 +/- 0.88ngmg(-1) respectively. UDCA is significantly more abundant in FF group than in SG group, and the total bile acids were higher in FF group than in SG group. Cetobacterium and Fusobacteriaceae U114 were significantly related with the concentrations of CDCA (r=0.85, P<0.05 and r=0.82, P<0.05 respectively) and UDCA (r=0.92, P<0.01 and r=0.92, P<0.01 respectively). However, Bacteroides was negatively related with the concentration of UDCA (r=-0.67, P<0.05). Overall, there existed certain relationship between the intestinal microbes and the faecal bile acids, and they were both influenced by the diet.