Abstract: Microbial community structure and composition difference are an effective indicator of the environmental health of marine ecosystems, which are crucial for ecological monitoring and management, as well as providing insight into aquaculture activities. In this paper, the gene sequencing and analysis were conducted to reveal the seawater microbial community structure of shellfish aquaculture and non-aquaculture area in Rizhao, and the effects of environmental factors on the microbial community structure and diversity were explored. Results showed that the most abundant microbial taxa in seawater from the aquaculture area were Proteobacteria, followed by Cyanobacteria and Actinobacteria. The relative abundance of Cyanobacteria (P=0.003) in the surface layer and Actinobacteria (P=0.027) in the 8-meter water layer were significantly higher in the aquaculture area than in non-aquaculture area. Microbial diversity analysis showed that from April to November, the Shannon values in the surface layer and the 8-meter water layer of aquaculture area were ranged from 5.59−6.92 and 5.33−7.08 respectively, which were not significantly different compared from those in the non-aquaculture area, but the microbial abundance in aquaculture area (Chao1=1088.86 in the surface layer, Chao1=1158.77 in the 8-meter water layer) was slightly lower than that in the non-aquaculture area (Chao1=1108.63 in the surface layer, Chao1=1210.30 in the 8-meter water layer). According to canonical correspondence analysis (CCA) and Spearman's correlation analysis, the temperature (P=0.003), salinity (P=0.001), suspended solids (P=0.001) and dissolved oxygen (P=0.001) were the main environmental factors affecting the microbial community structure in aquaculture area. In May, pathogenic bacteria of the genus Vibrio increased dramatically in 8-meter water layer of aquaculture area, with an average relative abundance of 51.21%, significantly higher than that of othe layers of aquaculture and non-culture area. This research will provide a reference for maintaining a healthy shellfish culture and protecting the ecosystem of aquaculture area.