Vibrio cholerae is a member of the Vibrionaceae family that is found in coastal waters and estuaries, and more than 200 serogroups have been identified. However, only two O-serogroups, O1 and O139, are associated with severe, life-threatening diarrheal disease cholera and responsible for its global pandemics. The epidemiological or genomic studies on O1 and O139 have been reported frequently, but the genetic diversity of V. cholerae population have yet to be elucidated and their understandings are limited. In this study, we performed a comprehensive genome analysis of O-serogroup reference V.cholerae strains to reveal the phylogenetic diversity and genomic characterization of V. cholerae population.