Abstract: In November 2018, surface seawater samples were collected from five characteristic stations in the Luoyuan Bay, Fujian Province, and the community structure and diversity among the samples were studied and analyzed by metagenomic sequencing. The results of the OTU number and α-diversity analysis showed that the number of bacteria in the five stations ranged from large to small as the sewage outlet > the dense living area > far away from the polluted area > marine outfall > the estuary of the thermal power station outlet. The five dominant phyla in the horizontal species abundance chart of the inner phyla of the bay were Proteobacteria, Bacteroides, Actinobacteria, Cyanobacteria and Firmicutes. Correlation analysis of environmental factors against the five dominant phyla showed that pH and inorganic nitrogen content were the main environmental factors affecting the distribution and diversity of microbial community in Luoyuan Bay.