Objective To understand the phenotypic diversity of toxigenic Vibrio cholerae O1 El Tor strains isolated from different provinces in China during the last 50 years. Methods Traditional biotyping testings including susceptibility to polymyxin B,sensitivity to groupⅣphage, Voges-Proskauer test and haemolysis of sheep erythrocytes were conducted. Results Data from Biotype-specific phenotype analysis revealed that only 133 isolates carryed the typical El Tor phenotypes while the other 251 isolates displayed atypical El Tor phenotypes. Combined with ctxB, rstR genotypes and phenotypic characteristics,64 isolates were identified as typical El Tor biotype,21 were El Tor variants that showing the typical El Tor biotype-specific phenotype but with ctxBclas . 280 isolates were defined as the hybrid groups with traits of both classical and El Tor biotypes that could be further classified into 45 groups,based on the combination of genotypes of ctxB,rstR and phenotypic characteristics. Conclusion Toxigenic Vibrio cholerae O1 El Tor strains that isolated from different provinces in China displayed high phenotypic diversity. The traditional biotype traits could not be used to correctly distinguish the two different biotypes.