Abstract: Objective The present study was conducted to analyze the NCA characteristics of Vibrio cholerae O139 strains isolated from environment-derived samples in Jiangsu from 2003 to 2005 and determine whether there was variance and its' variation degree. Methods The combined comparison and analysis were conducted on the phenotype characteristics (including: serotype; drug fast spectrum; biochemical characteristics and the phage typing of El Tor Vibrio cholerae) and NCA characteristics (including: distribution state of choleratoxin genes ctx-A、zot、ace、tcp-A and pulsed field gel electrophoresis fingerprint) of 11 objective strains. Results Among 11 strains,10 strains were O139 isolates Vibrio cholerae and 1 strain was El Tor; of which 6 O139 strains resisted more than 5 antibiotics, 2 O139 strains resisted 4 antibiotics, 1 O139 strain resisted 2 antibiotics, and the last one O139 and one El Tor resisted only one antibiotic respectively; no significant variance in biochemical characteristics was found among all the strains, of which 8 strains O139 possessed 4 toxicity-related genes, 1 O139 strain only possessed zot and ace genes and another O139(05052) strain and 1 El Tor had none of the 4 genes; There were two types of pulsed field gel electrophoresis fingerprints, 9 strains were classified to one type and the other two were to another type. Conclusion One O139 strain (Type PFGE-C) was different from the other 9 strains in drug-fast spectrum and toxicity-related gene distribution but was similar to one El Tor strain isolated at the same place, which indicated that variance could be found among the Vibrio cholerae O139 strains living in natural environment.