Aims To identify the intestinal microbial diversity in mud crab and to investigate the bacterial difference in the intestinal microbiology between wild crabs (WC), pond-raised healthy and diseased crabs (DC). Methods and Results The intestinal microbial community of mud crab Scylla paramamosain from WC, pond-raised healthy crabs (HC) and DC were examined by Denaturing Gradient Gel Electrophoresis (DGGE) and clone library analysis of 16S rDNA gene. Eight of 21 representative DGGE bands were affiliated with unidentified or unclassified bacteria. Vibrio, Pseudoalteromonas and Shewanella were also found from the DGGE gel. Analysis of clone libraries revealed that all sequenced clones were grouped into either of the following phyla: Proteobacteria, Firmicutes, Tenericutes, Bacteroidetes, Fusobacteria, Cyanobacteria and unidentified or unclassified bacteria. The phylotypes affiliated with Firmicutes were not found in DC library, yet DC had a little portion of Cyanobacteria which did not exist in both WC and HC library. Real-time PCR showed that the abundance of the total bacterial load in WC were significantly three times higher than that in healthy and DC, the abundance of Bacteriodes in healthy and WC were as much four times, three times as that in DC, respectively. Conclusions Statistical analysis showed that the bacterial communities in intestine of the mud crab from these three populations were significantly different. The phylotypes of the Bacteriodes and Tenericutes were the dominant population in the gut of the mud crab. Significance and Impact of the Study This study demonstrated significant differences in the intestinal bacterial composition of three crab populations. This knowledge will increase our understanding of the effect of growth conditions on bacterial community composition in the crab gut and provide necessary data for further development of probiotic products for diseases prevention in crab farming.