Abstract: Ship ballast water directly promotes the water exchange between geographically isolated sea areas and has been regarded as a medium for the migration of potential pathogenic bacteria. In this study, 25 ballast water samples of entry ships were collected and high-throughput sequencing technology was used to analyze the composition and influencing factors of potential pathogenic bacteria. The results showed Proteobacteria, Bacteroidetes and Actinobacteria were the dominant bacteria in ship ballast waters. A total of 36 genera and 19 species of potential pathogenic bacteria were detected in the ballast waters. Cutibacterium acnes, Escherichia coli and Staphylococcus epidermidis were the most common pathogens with the detection rate exceed 50% in ship ballast waters. No significant difference was found for the species number and abundances of potential pathogenic bacteria between the exchanged and unexchanged ballast waters. The close positive relationship between pathogenic bacteria and phosphorus and Escherichia coli indicated that human activities should be an important factor for those pathogens in ballast waters. In all, it should strengthen the management of ballast water so as to reduce the invasion risk of potential pathogenic bacteria.