Silver carp is one of the most important planktivorous fish in Chinese aquaculture and plays a significant role controlling cyanobacterial blooms. A balanced gut microbiota is crucial for growth and health of the host because of its important roles in immune defense, digestion of complex carbohydrates, and production of enterocytes. In our study, the dominant bacterial and cellulolytic bacterial (Clostridium I, Clostridium III, Clostridium XIVab, and Fibrobacter) communities in the contents and mucus of the silver carp gut (foregut, midgut, and hindgut) were analyzed by denaturing gradient gel electrophoresis and quantitative polymerase chain reaction (qPCR) analyses. The results revealed that the dominant and cellulolytic bacterial communities were significantly different among gut regions as well as in contents and mucus. Bacterial diversity and richness in contents and mucus increased along the gut and were higher in contents than those in local mucus. A sequence analysis of gut samples exhibited the conservative phylotypes of Proteobacteria, Actinobacteria, and Firmicutes. The gut of silver carp harbored an abundance of cellulolytic bacteria, particularly Clostridium XIV ab. The foregut segment had the highest proportions of the four cellulolytic bacteria, followed by the midgut and hindgut. However, the proportions of cellulolytic species in the silver carp gut was much lower than those in the terrestrial vertebrate gastrointestinal tract. We conclude that gut bacteria could help silver carp obtain energy from cyanobacteria, which may be why silver carp can maintain high growth rates during cyanobacterial blooms.