AimsA study was conducted to compare the intestinal microbial compositions of two fish species with similar feeding strategy; paddlefish (Polyodon spathala) and bighead carp (Aristichthys nobilis) reared in the same pond. Methods and ResultsAge-0 paddlefish and bighead carp with mean average body lengths of 4339278 and 1933368cm, respectively, were reared with natural prey items in the same pond (20m(2)). After 30days of rearing, the intestinal microbiota of the two fish species was assessed by pyrosequencing of 16S rRNA genes. Interestingly, deviations were observed in the microbial communities of the two fish species according to the alpha- and beta-diversity measurements and detrended correspondence analysis (DCA). Shannon diversity (P=0015) and Pielou.evenness (P=0035) revealed significant lower diversity of the intestinal microbiota of paddlefish. Moreover, different core intestinal microbiota was noticed in the two fish species. Proteobacteria (573%), Firmicutes (119%), Fusobacteria (89%), Planctomycetes (73%), Actinobacteria (60%) and Verrucomicrobia (32%) were detected in bighead carp, while the dominant phyla in paddlefish intestines were Bacteroidetes (370%), Fusobacteria (351%), Firmicutes (148%) and Proteobacteria (126%). ConclusionsOur results revealed that the intestinal microbiota differed between paddlefish and bighead carp reared in the same pond when fed similar nature food. The potential host factors, such as the genetic background, gut histology and physiology are assumed to be involved in the intestinal bacterial compositions. Significance and Impact of the StudyConsidering the similar feeding strategy of paddlefish and bighead carp, this study presents basic knowledge for evaluation of the importance of host factors (genetic background and gut anatomy) on intestinal microbial composition.