Abstract: Bacteria play a key role in the biological geochemical cycle and degradation of organic contamination in pond ecosystem. It is important to understand the dynamics of bacterial community structure in recirculating aquaculture system during shrimp and shellfish rearing. In this study, bacterioplankton community structure in mangrove constructed wetland-mariculture coupling system was investigated by using high-throughput sequencing with 16S rDNA. High-throughput sequencing analysis indicated that the dominant OTUs were Proteobacteria, Cyanobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Planctomycetes. Proteobacteria and firmicutes were the most dominant phyla in mangrove wetland, while bacteroidetes and planctomycetes were the most abundant in shrimp pond. The analysis of Shannon-Wiener indices inferred that proteobacteria communities were the highest, whereas firmicutes were the lowest. The diversity of bacterial phyla in shrimp pond was lower than that of the other station (except firmicutes), whereas the diversity of bacterial phyla in mangrove wetland was higher than that of the other station (except actinobacteria). Multidimensional scaling revealed the changes in the microbial community structure of different stations. The microbial community structure in shrimp pond was markedly different from other stations in recirculating mariculture system, suggesting that shrimp farming has a great influence on bacterioplankton community structure.