Abstract: Objective To screen the O139 serogroup Vibrio cholerae strains that can produce brown pigment and analyze the clonality of these pigment producing strains. Methods A total of 1530 strains of O139 V. cholerae were detected to understand their ability to produce soluble brown pigment. Their homogentisate oxygenase genes (VC1345) were sequenced and their clonality relation was analyzed by PFGE typing and MLST. Results Sixteen strains of pigment producing but non-toxin producing O139 V. cholerae strains isolated in 3 provinces in 13 years were selected. They had completely same VC1345 gene, highly similar PFGE type, and two kinds of MLST types. Conclusion All of the pigment producing O139 V. cholera strains isolated in outer environment came from one phylogenetic clone group with low degree diversity. The sustained existence of such strains in outer environment indicates that they may have strong survival ability, suggesting that close attention should be paid to such strains in the surveillance of V. cholerae.