Abstract: To investigate the bacterial diversity of surface seawater of the Yongle atoll, Illumina MiSeq sequencing was used to analyze the bacterial communities of six islands. The main environmental impact factors were explored and the functions were also predicted. A total of 891 892 high-quality sequences and 7 499 optimized OTUs were obtained. These OTUs were identified to belong to 49 phyla, 144 classes, 392 orders, 663 families, and 1 274 genera. The bacteria communities were dominated by Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacteria, Patescibacteria and Firmicutes. Redundancy analysis revealed that the conductivity, pH and temperature were the main environmental factors affecting the microbial assemblages. The PICRUSt analysis showed that 6 functional modules and 46 functions at level 2 were predicted; A total of 399 at level 3 pathways were obtained, of which the most abundant pathways were metabolic pathways and the biosynthesis of secondary metabolites. This study analyzed the surface seawater bacterial community and gene function prediction of six islands from Yongle atoll, providing basic data for further investigation and development of microbial resources.