In order to investigate the effects of different aquacultural species (Procambarus clarkii, PC and Pelodiscus sinensis, PS) on planktonic and benthic bacterial communities, water and sediment samples were collected. The α-diversity, compositions and abundance of the planktonic and benthic bacterial community were analyzed using high-throughput sequencing targeted the 16S rRNA genes. The influence of environmental factors on bacterial communities was also examined. The results showed that, for both water and sediment samples, the α-diversity of bacterial community within PS zone was significantly higher than that of the PC zone (P<0.05). Nonmetric multidimensional scaling (NMDS) analysis showed that the bacterial community composition of the water and sediment samples were significantly different between the two zones. Redundancy analysis (RDA) showed that ammonia nitrogen (NH₄⁺-N) and nitrate nitrogen (NO₃^--N) were the main factors that affected the bacterial community composition in the water samples. Total nitrogen (TN), total phosphorus (TP), and organic carbon (OC) had significant effects (P<0.05) on the bacterial community composition in the sediment samples. 34 phyla, 114 classes, 258 orders, 504 families, and 955 genera of bacterial communities were obtained totally from the water and sediment samples in the two zones. High-throughput sequencing analysis indicated that there were eleven and thirteen dominant phyla (relative abundance>0.5%) of bacterial communities within water and sediment samples, respectively. We found fifteen and seven dominant (relative abundance>1%) operational taxonomic units (OTUs) in water samples and sediment samples, respectively. In water samples, there were nine dominant OTUs could remove nutrients, and they were belonged to Comamonadaceae, Saprospiraceae, Methylophilus, Actinomycetales and Sediminibacterium, respectively. The relative abundance of these nine dominant OTUs within PC zone was higher than that of the PS zone in general. And the relative abundance of the eight of them was significantly positively correlated (P<0.01) with NH₄⁺-N and NO₃^--N. In sediment samples, there were three dominant OTUs played important roles in the nitrogen cycle, and they were belonged to Dechloromonas, Prolixibacteraceae and Anaerolineaceae, respectively. Furthermore, three dominant OTUs in water samples were detected as pathogens, which belonged to Flavobacterium and Polynucleobacter, respectively. Pearson correlation analysis demonstrated that the relative abundance of the three dominant OTUs which were detected as pathogens were significantly positively correlated (P<0.01) with NH₄⁺-N and NO₃^--N. Based on the above results, different aquacultural species had different effects on bacterial community diversity and composition of water and sediment.