[Background] Although microbial community in polyculture environment and animal intestines have been reported in previous studies, relationship of microbial community between intestinal microflora and polyculture environment needs to be deeply studied. [Objective] To study microbial communities of shrimp and clam intestine associated with polyculture environment. [Methods] Illumina sequencing was used to identify shift of taxonomic diversity among samples collected from two polyculture ponds in Putian. [Results] Bacterial community of shrimp intestine had very high similarity with clam intestine collected from two different polyculture pond. Shannon and Chao1 estimator supported the diversity results and suggested that the bacterial community in pond sediments was richer than those in pond water and animal intestine. Furthermore, bacterial community of animal intestines was dominated by Firmicute and Gammaproteobacteria, and culture water was dominated by Actinobacteria, Alphaproteobacteria and Bacteroidete, as well as by Gammaproteobacteria and Deltaproteobacteria in the underlying sediment. High abundance of potential probiotics, such as Lactococcus and Pseudomonas, was detected in animal intestine. Conditional pathogenic bacteria (such as Flavobacterium) had high abundance in polyculture environment, whereas little pathogenic bacteria were detected in animal intestine. Finally, high abundances of sulfate-reducing bacteria were found in the pond sediments, which may cause serious harm to aquaculture environment through producing hydrogen sulfide. [Conclusion] This study explores the significant difference of microbial community between polyculture environment and animal intestines and revealed the effect of polyculture environment on intestinal microflora. This study will provide reference for the optimization of polyculture structure and the diseases prevention of aquaculture animals.