The diversity of microbes plays a dominant role in maintaining stability of marine ecosystems. In this study, the author applied 16S rRNA gene-based Illumina Miseq to reveal the microbial diversity of Dapeng Bay and Shenzhen Bay and to predict the ecological function of microbial communities of the two seawater. The results indicated that the Shannon, Simpson, Chao1, and ACE diversity index and OTUs numbers in Dapeng Bay were much higher than those in Shenzhen Bay. The microbial communities of Dapeng Bay and Shenzhen Bay could be classified into 24 and 10 phyla, respectively. The dominant phyla were Cyanobacteria, Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, Planctomycetes in the seawater of Dapeng Bay and Shenzhen Bay, which accounted for 99.3% and 99.9% of their microbial communities. However, the relative abundance of these phyla in these two seawater was different. The microbial communities classified in order, class, family, genus levels showed different patterns in the seawater of Dapeng Bay and Shenzhen Bay. The genus Prochlorococcus (60.0%) belonging to phylum Cyanobacteria dominated the microbial community in Shenzhen Bay, where the uncultured bacterium of Cyanobacteria dominated the microbial community in Dapeng Bay. The prediction of the metabolic function by using PICRUSt indicated that there was a difference in the metabolic functions of seawater microbes in Dapeng Bay and Shenzhen Bay，which were significantly distinct in the metabolisms of biodegradation, lipid metabolism, enzyme families and carbohydrate metabolism. This study provides the scientific basis for marine microbial diversity and marine ecosystem protection.