To investigate bacterial communities and diversity in the shrimp(Penaeus penicillatus)intestinal and culture-associated environment,16S rRNA clone library analysis was performed.The results demonstrated that there were obvious differences in the bacterial compositions of the outside seawater,culture system and the shrimp intestine.The comparison analysis revealed that the bacterial community had high diversity among the samples.The results also showed that the intestinal microbial community of shrimp had lower diversity than those from the culture-associated environments.Cyanobacteria(53.97%),Alpha-proteobacteria(13.76%)and Gamma-proteobacteria(10.58%)constituted the dominant components of the outside seawater samples.Cyanobacteria(33.55%),Gamma-proteobacteria(14.84%),Firmicutes(14.19%),Bacteriodietes(12.26%)and Alpha-proteobacteria(9.68%)were the dominant bacteria groups in culture water.Culture sediments were mainly dominated by Firmicutes(79.12%).Firmicutes(75.79%),Fusobacteria(13.68%)and Gamma-proteobacteria(10.53%)were dominant in the shrimp intestine.The order of Bacillales occupied a higher proportion of bacterial community in culture sediments(69.78%),culture water(13.55%)and the shrimp intestinal tract(72.63%),which may play an important role in the maintenance of healthy culture system.An important bacteria group,Rhodobacterales was also dominant in outside water(10.05%)and culture water samples(9.68%).In addition,outside seawater and culture water harbored higher diversity of bacterial community than the shrimp intestine and culture sediments,and had more potential pathogens,such as Flavobacteria(10.32%)and Fusobacteriales(13.68%).This study will increase our understanding about the effects of culture environment on bacterial community composition in the shrimp intestine and provide valuable data for the development of prevention mechanisms for shrimp cultivation.