In order to explore the effect of Enteromorpha bloom on the bacterial community, Illumina MiSeq Sequencing was used to investigate the bacterial structure in source water, culture pond and drainage area in this study. The results showed that Gammaproteobacteria, Alphaproteobacteria, Actinobacteria, Bacteroidete and Deltaproteobacteria were the dominant bacteria groups in aquaculture water. Bacterial community in source water had higher in species numbers and Shannon diversity than pond and drainage area with Enteromorpha. Furthermore, pond and drainage area with Enteromorpha was dominated by heterotrophic bacteria in water (mainly Actinomycetales and Flavobacteriales), as well as by anaerobic bacteria in underlying sediment (mainly Desulfobacterales), which increased potential ability to produce hydrogen sulfide. Source water contained high abundance of conditional pathogenic microbe, such as vibrio and Piscirickettsiaceae; whereas little was detected in Enteromorpha-containing pond,which indicated that Enteromorpha had strong inhibitory effect on these pathogens. In addition, Enteromorpha also increased the abundance of Flavobacterium in pond and drainage areas; some genera of Flavobacterium are conditional pathogenic bacteria for aquaculture animal, and need pay attention to prevent such infections disease. Enteromorpha has the dual role to inhibit or increase abundance of different pathogens, and have importance effect to aquaculture. Overall, massive growth of Enteromorpha would produce the significant effect on the bacterial community, and have serious impact on the coastal environment. This study explored the novel findings of the microbial community relevant to Enteromorpha, and will provide guidance for the prevention and control of the green tide.