[Background] Sustainable development of coastal ecosystem has become one of the most important concerns for people nowadays. Riverine output and anthropogenic interrupt have important impacts on the coastal environment. [Objective] In this study, we collected 12 samples from three transects including Bohai Bay, Liaodong Bay and Laizhou Bay to explore the microbial community and diversity in summer of 2015. [Methods] DNA was extracted from water samples by using DNA extraction kit. Samples were analyzed by Illumina HiSeq sequencing technology. We compared the differences among these three transects according to the analysis results. [Results] The diversity index and rarefaction curves showed significant differences among these three transects. The order of diversity value was Laizhou Bay>Bohai Bay>Liaodong Bay. The distribution of the dominant community was as follows: the proportion of Proteobacteria, Bacteroidetes, Cyanobacteria, Actinobacteria and Planctomycetes in the Bohai Bay was 39.8%, 25.7%, 22.4%, 5.85% and 4.38%, respectively. The dominant community proportion in Liaodong bay was Proteobacteria (37.8%), Bacteroidetes (25.7%), Cyanobacteria (17.8%), Actinobacteria (10.4%) and Planctomycetes (5.64%). While in Laizhou Bay there were only four dominant communities as follows: Proteobacteria (59.0%), Bacteroidetes (17.5%), Cyanobacteria (8.2%), Actinobacteria (7.88%). By using the principal component analysis (PCA) and Heatmap correlation analysis, we found that environmental factors were key roles in controlling the microbial diversity in the Bohai Sea. Among them, the concentration of nitrate was particularly significant according to the Mantel test analysis. [Conclusion] The microbial diversity in the three bays of Bohai Sea was very rich and multifarious. The population structure and species in the Laizhou Bay is the most complex and abundant among these three bays, and then it is Bohai Bay and Liaodong Bay. There was a significant correlation among microbial diversity, environmental factors and the spatial distribution. Above all, this study will provide a theoretical basis for further protection and ecological development of Bohai Sea
