Abstract: In this study, crayfish from Huoqiu in Anhui Province, Xuyi in Jiangsu Province, and Jingzhou in Hubei Province were selected as the research objects. Environmental samples of two modes of rice-shrimp co-cropping and aquaculture ponds were taken from Jingzhou. High throughput technology was used to analyze the bacterial diversity, and culture-dependent method was used to isolate, purify and identify the bacteria to verify the type and quantities of dominant bacteria. The results showed that the initial bacterial count of Jingzhou crayfish was slightly lower than that of Xuyi and Huoqiu crayfish, and the difference in the selection medium was small. The results of high-throughput sequencing showed that the dominant of four samples groups bacteria were Aeromonadaceae and Enterobacteriaceae. The abundance of soil microbial community in rice shrimp pond was much higher than that in aquaculture pond, and the microbial community in water was similar. At the genus level, there were differences in the abundance of bacteria in four samples groups of crayfish samples from Jingzhou rice shrimp pond, aquaculture pond, Xuyi and Huoqiu, However, both Aeromonas and Acinetobacter accounted for a higher proportion, followed by 41.8%, 1.8%, 12.4%, 11.4%, 24.5%, 27.5%, 40.1%, 13.0%. The dominant bacteria of crayfish in Jingzhou rice shrimp pond also included Lactococcus and Citrobacter, and the strains of Hafnia and Lactococcus were found in the aquaculture pond samples. The predominant bacteria in Xuyi and Huoqiu crayfish samples were Exiguobacterium and Citrobacter. The culture-dependent results showed that the dominant bacteria were Aeromonas, Hafnia and Citrobacter, which were consistent with the high-throughput results.