Abstract: To reveal the impacts of different section in mariculture wastewater treatment system on microbial community, the microbial community structure of water and biofilm was analyzed by 16S rRNA gene high-throughput sequencing technology. The results showed that the dominant microbial phyla in the water treatment system included Proteobacteria, Planctomycetes, Bacteroidetes, Cyanobacteria, Actinobacteria and Acidobacteria, which accounted for 88.61% on average. The biodiversity index of biofilms was higher than that of water, and there were 320 common bacteria in all samples. The reason lead to difference of community structure between biofilms was the physical material, ceramsites and Salicornia bigelovii root were the main reaction site for nitrification. At genus level, 160 bacterial OTUs were selected to distinguish the source of bacterial populations and the period of biofilms in water treatment system. These 160 species mainly include Proteobacteria, Bacteroides, Fusarium, Cyanobacteria, Firmicutes and Actinomycetes. This study revealed the dynamic characteristics of bacteria in different wastewater treatment periods and different biofilms, and provided theoretical basis and technical reference for improvement of maricultrue wastewater treatment system.