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Background. Quinolones are commonly used for reducing the duration of diarrhea, infection severity, and limiting further transmission of disease related to <i>Vibrio cholerae</i>, but <i>V. cholerae</i> susceptibility to quinolone decreases over time. In addition to mutations in the quinolone-resistance determining regions (QRDRs), the presence of <i>qnr</i> and other acquired genes also contributes to quinolone resistance. Results. We determined the prevalence of quinolone resistance related genes among <i>V. cholerae</i> O139 strains isolated in China. We determined that eight strains carried <i>qnrVC</i>, which encodes a pentapeptide repeat protein of the Qnr subfamily, the members of which protect topoisomerases from quinolone action. Four <i>qnrVC</i> alleles were detected: <i>qnrVC1</i>, <i>qnrVC5</i>, <i>qnrVC12</i>, and <i>qnrVC9</i>. However, the strains carrying <i>qnrVC1</i>, <i>qnrVC5</i>, and <i>qnrVC12</i> were ciprofloxacin (CIP)-sensitive. Contrastingly, the strain carrying <i>qnrVC9</i> demonstrated high CIP resistance. <i>qnrVC9</i> was carried by a small plasmid, which was conjugative and contributed to the high CIP resistance to the receptor <i>V. cholerae</i> strain. The same plasmid was also detected in <i>V. vulnificus</i>. The <i>qnrVC1</i>, <i>qnrVC5</i>, and <i>qnrVC12</i> were cloned into expression plasmids and conferred CIP resistance on the host <i>V. cholerae</i> O139 strain. Conclusions. Our results revealed the contribution of quinolone resistance mediated by the <i>qnrVC9</i> carried on the small plasmid and its active horizontal transfer among <i>Vibrio</i> species. The results also suggested the different effects of <i>qnrVC</i> alleles in different <i>V. cholerae</i> strains, which is possibly due to differences in sequences of <i>qnrVC</i> alleles and even the genetic characteristics of the host strains.