Mud crab (), widely cultured in brackish and seawater ponds along the coast of southern China, has become the most productive seawater crab species because of its strong adaptive abilities and high economic value. Bacteria play an important role in pond aquaculture ecosystems; however, little is known about the bacterial composition and diversity in earthen aquaculture pond microbial communities of . Accordingly, we applied Illumina HiSeq high-throughput sequencing to investigate bacterial community structure and diversity in pond-raised intestinal and its aquacultural environment. The results showed that 234575 effective sequences were detected in three samples, and they could be classified into 2812 operational taxonomic units (OTUs), among which 453, 706, and 2547 OTUs belong to the gut of , the aquaculture water, and the sediment, respectively. 184 OTUs were shared among all samples, 197 OTUs between S. paramamosain intestine and sediment, and 572 OTUs between the aquaculture water and sediment. This indicates that bacterial richness and diversity were lower in intestine than in water and sediment. In total, 48 phyla were identified, among them Proteobacteria (39.96%), Tenericutes (23.09%), Firmicutes (16.58%), CKC4 (6.55%), and Bacteroidetes (4.96%), which constituted the predominant components of the intestine; Proteobacteria (63.02%), Actinobacteria (24.96%), Bacteroidetes (8.41%), Cyanobacteria (1.19%), and Firmicutes (0.83%) were the predominant phyla in the water; and the predominant phyla in the sediment were Proteobacteria (75.23%), Bacteroidetes (5.72%), Actinobacteria (3.83%), Chloroflex I (2.65%), and Acidobacteria (1.80%). Analysis of the 10 most abundant bacterial OTUs in different samples revealed that the most dominant bacteria in intestine and its aquacultural environment were totally different, and there were only four kinds of dominant bacteria that have close sequences in the SILVA database. These results suggest that there exists a close correlation between bacterial species composition in the intestine and its aquacultural environment. Meanwhile, intestinal microflora may be a relatively independent microbial ecosystem and the micro-ecosystem could hardly be influenced by the bacteria in the culture environment.