Abstract:Zostera japonica is a unique Asian seaweed species and has important ecological value. In recent years, Zostera japonica has been continuing to degenerate, causing widespread concern among researchers. [Objective] We hypothesized that the rhizospheric microorganisms were closely related with the healthy growth of Zostera japonica. We explored the diversity and function of microbial community in root of Zostera japonica at coastal zone of Yellow sea and Bohai sea, and intrinsic relationship with seagrass.[Methods] We collected surface sediment samples of Zostera japonica roots and unvegetated areas from three locations including Dongying, Weihai, and Dalian city. We investigated the rhizosphere microbial community structure by sequencing on Illumina HiSeq300 platform and analyzed the correlation between microbial community structure and environmental parameters. [Results] The most dominated phyla widely distributed in the rhizospheric surface sediments of Zostera japonica included:Proteobacteria (41.1%), Cyanobacteria (15.4%), Bacteroidetes (12.6%), Actinobacteria (9.3%). Comparisons of different regions (Weihai, Dongying, and Dalian) or sample types (rhizosphere vs. non-rhizosphere) showed significant differences in microbial communities, mainly due to the presence of sulfate-reducing bacteria and nitrogen-fixing bacteria found in the rhizosphere. Total nitrogen, total carbon, total organic carbon, clay, were all significantly correlated to rhizospheric bacterial community composition and distribution. [Conclusion] From a functional point of view, the differences between groups was mostly related to sulfur and nitrogen cycling, and sulfate reducing bacteria play a key role in maintaining the ecological health of Zostera japonica.