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Aims:  To identify the dominant intestinal bacteria in the Chinese mitten crab, and to investigate the differences in the intestinal bacteria between pond‐raised and wild crabs. Methods and Results:  The diversity of intestinal bacteria in the Chinese mitten crabs was investigated by denaturing gradient gel electrophoresis (DGGE) fingerprinting, 16S rRNA gene clone library analysis and real‐time quantitative PCR. The principal component analysis of DGGE profiles indicated that substantial intersubject variations existed in intestinal bacteria in pond‐raised crab. The sequencing of 16S rRNA genes revealed that 90–95% of the phylotypes in the clone libraries were affiliated with Proteobacteria and Bacteroidetes. Some genera were identified as unique in wild crabs and in pond‐raised crabs, whereas Bacteroidetes was found to be common in all sampled crab groups. Real‐time quantitative PCR indicated that the abundance of Bacteroides and the total bacterial load were approximately four‐to‐10 times higher in pond‐raised crabs than in wild crabs. A significant portion of the phylotypes shared low similarity with previously sequenced organisms, indicating that the bacteria in the gut of Chinese mitten crabs are yet to be described. Conclusions:  The intestinal bacteria of pond‐raised crabs showed higher intersubject variation, total diversity and abundance than that observed in wild crabs. The high proportion of the clones of Proteobacteria and Bacteroidetes in the clone library is an indication that these bacteria may be the dominant population in the gut of the Chinese mitten crab. Significance and Impact of the Study:  This study demonstrated obvious differences in the intestinal bacterial composition of pond‐raised crabs and wild crabs. This knowledge will increase our understanding of the effects of aquaculture operations on bacterial community composition in the crab gut and provide necessary data for the development of probiotic products for crab cultivation.

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