The difference of initial microbial communities of crayfish （Procambarus clarkii） from different origins of Pukou and Dongshan was studied using culture-dependent method and metagenomic analysis in this study. The results showed that the initial total bacterial counts of whole crayfish samples of Pukou and Dongshan was not significant different， but the bacterial counts on the selective enrichment cultures were not significant different. It was found that Aeromonas and Citrobacter were the dominant bacteria in the total samples of Pukou crayfish， Hafnia paralvei was the domain bacterium in the total samples of Dongshan crayfish by 16S rRNA gene analysis. At family level， Enterobacteriaceae strains were the domain bacteria of the total samples from these two regions. At genus level， Aeromonas and Exiguobacterium were dominant bacteria in total samples from Pukou crayfish， and Flavobacterium， Aeromonas and Shewanella were the domain bacteria in the total samples of Dongshan crayfish. The results of the initial bacterial diversity of different parts of crayfish （Procambarus clarkii） from different origins indicated that the potential food safety risk of crayfish， and provided a reference for the future study of crayfish preservation and transportation.