The formation and regulation of vertebrate endogenous intestinal microbiota has been widely studied as the microbiota plays a crucial role in the host nutrition, development, and health. Despite the importance of microbiota for host health, it is still unclear whether the endogenous intestinal microorganisms are genetically distinct or whether they are genetically related with each other in different host individuals. In the present study, the dispersal situation of the endogenous intestinal bacteria in grass carp was investigated by constructing bacterial 16S rRNA gene clone libraries. The results indicate that the bacteria harbored in the grass carp gut could be separated into the following two groups: a- the private operational taxonomic units (OTUs), which include Cetobacterium somerae, Aeromonas jandaei, Citrobacter freundii, Achromobacter xylosoxidans and Bacteroides species; b- the shared OTUs, which include Vibrio cholerae, Plesiomonas shigelloides and Pasteurella speices. The results obtained in this investigation provide valuable information for assessing the mechanism of spread of the endogenous intestinal bacteria, especially the pathogenic ones. However, the mechanisms involved in different modes of bacterial dispersal in the grass carp gut still require further research.