To investigate the bacterial species composition and distribution in the intestine of Boone and its aquacultural environment, we used Illumina MiSeq high-throughput pyrosequencing to analyze the composition of the bacterial communities in the gut of Boone and its aquacultural sediments and water, based on the 16S rRNA sequence. We detected 206, 265, and 270 genera in the gut of Boone, the aquaculture sediment, and the water, respectively. Ninety genera occurred in all three samples, 146 genera in the sediment and water, 128 in the sediment and intestine. This indicates the close interaction between the bacteria in the shrimp intestine and their aquacultural environment. Twenty, seventeen, and ten dominant genera with a relative abundance in the total sequences of > 1% occurred in the sediment, water, and intestine, respectively. Unclassified genera were the most abundant in all the samples, accounting for 23.08%, 37.13%, and 42.22% of the total sequences from the sediment, water, and Ohtaekwangia (4.79%), and Sediminibacterium (6.64%), (3.95%), and GPIIa (3.20%) were the dominant genera in water; and the predominant genera in the Acinetobacter (6.54%). Three, three, and six potentially pathogenic bacterial genera were also observed in the sediment, water, and Boone intestine, respectively, and the most abundant were (14.57%), respectively. Six, eight, and seven probiotic genera were also found in the sediment, water, and Boone intestine, respectively, and among these genera, five were shared by all three samples. A cluster analysis showed that the 20 most abundant operational taxonomic units in each sample (sediment, water, and Boone intestine) differed significantly. These results provide insight into the interactions between the microbiota in the intestine of Boone and those in its aquacultural environment, and provide new data for the development of probiotics.