Objective To understand the distribution,molecular characteristics and virulencegenes of the O1 and O139 Vibrio cholerae isolates from the Pearl RiverEstuarywater.MethodsVibrio cholerae isolates collected from the Pearl Riverestuary waters from January 2009 to December 2010,were tested by PCR for eight virulence-related genes,including cholera toxin(ctxA),zonula occludens toxin(zot),accessory choleraenterotoxin(ace),hemolysin(hlyA),toxin-coregulated pilus (tcpA),outer membrane protein(ompU),and the regulatory proteingenes(tcpⅠ,toxR).Genetic relation was assessed by pulsed-field gel electrophoresis(PFGE)and the patterns were clustered by BioNumerics.Results From 1152 aquatic samples,69 isolates were identified,including 41 Inaba,18 Ogawa and 10 O139.All the isolates showed ctxA negative,while the hlyA and toxR genes were positive in all the isolates.34.15%(14/41)of the Inaba strains were hlyA + toxR + ompU + ace + zot + tcpI+,while 66.67%(12/18)belonged to Ogawa strains and 70%(7/10)of the O139 strains were hlyA + toxR+.Through PFGE analysis,the O1 isolates formed three clusters in this study.The patterns of O1 isolates differed widely,with the similarity as 72.8%-100.0%,while the patterns of O139 isolates having the similarity of 69.9%-95.5%.Conclusion The non-toxigenic O1 and O139 V.cholerae had a wide distribution in the environment of Pearl Riverestuarywater during the nonepidemic period of cholera.All the aquatic isolates presented diversities on the related virulent genes.