| Summary: | <i>Vibrio vulnificus</i> is a gram-negative, opportunistic human pathogen associated with life-threatening wound infections and is commonly found in warm coastal marine water environments, globally. In this study, two fishing harbors and three tributaries of the river basin were analyzed for the prevalence of <i>V. vulnificus</i> in the water bodies and shellfish that are under the pressure of external pollutions. The average detection rate of <i>V. vulnificus</i> in the river basins and fishing harbors was 8.3% and 4.2%, respectively, in all seasons. A total of nine strains of <i>V. vulnificus</i> were isolated in pure cultures from 160 samples belonging to river basins and fishing harbors to analyze the antibiotic susceptibility, virulence gene profiles, and enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) fingerprinting. All isolates were susceptible to 10 tested antibiotics. The genotypic characterization revealed that 11.1% (<i>n</i> = 1/9) strain was nonvirulent, whereas 88.9% (<i>n</i> = 8/9) isolates were virulent strains, which possessed the four most prevalent toxin genes such as <i>vcgC</i> (88.9%), <i>16S B</i> (88.9%), <i>vvhA</i> (88.9%), and <i>manIIA</i> (88.9%), followed by <i>nanA</i> (77.8%), <i>CPS1</i> (66.7), and <i>PRXII</i> (44.4%). Additionally, ERIC-PCR fingerprinting grouped these nine isolates into two main clusters, among which the river basin isolates showed genetically diverse profiles, suggesting multiple sources of <i>V. vulnificus</i>. Ultimately, this study highlighted the virulent strains of <i>V. vulnificus</i> in the coastal aquatic environments of Taiwan, harboring a potential risk of infection to human health through water-borne transmission.
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