Abstract: In this study, 16S rRNA gene sequencing was used to analyze the community structure of potential pathogenic bacteria in the typical tropical (Xincun, Li'an, Tanmen) seagrass meadows of the South China Sea. The abundances of Vibrio and Enterococcus were counted by selective medium analysis, and their typical virulence genes abundances were quantified by quantitative PCR. The results show that the putative bacterial pathogens in Xincun and Li'an clustered and then separated from those of Tanmen. Abundances of cultured Vibrio and Enterococcus, and the typical virulence genes contents of vhh, toxR, aspA, esp, and gelE followed a descending order of Xincun>Li'an>Tanmen, while the contents of Vibrio typical virulence genes of ctxA, tlh, trh, and vvp followed a descending order of Tanmen>Xincun> Li'an. Higher intensity human activities, such as nutrient load, probably are responsible for the higher abundance of pathogens and virulence genes of seagrass meadows in Xincun and Li'an, while the differences between Xincun and Li'an may be attributed to different types of human activities.