Abstract:In order to explore its pathogenicity differentiation, the 15 representative strains of Verticillium dahliae in cotton were determined by cultural characteristic observation,pathogenicity testing and ISSR molecular marking analysis. Results showed that there was the positive correlation of growth rate and conidia production of strains of V.dahliae to its pathogenicity. Pathogenicity differentiation of representative strains of V.dahliae tested with five cotton differential hosts was obviously found: TypeⅠcausing a severe defoliation with strong pathogenicity, TypeⅡ causing with weak pathogenicity, TypeⅢ causing with inter-mediate pathogenicity. Among them, strains of TypeⅠ, TypeⅡ and Type Ⅲ occupied 46. 67%, 20.0% and 33.3% of total examined strains and the average disease index of them was more than 36.1, less than 21 and between 20 to 28, respectively. The 623 bands were obtained by PCR amplification with 4 ISSR primers, which there were 425 polymorphic bands. The strains of V.dahliae were clustered into 2 genetic lineages at 0.55 genetic similarity and it showed that there were some relations of genetic lineages of V.dahliae to its geographical origin, pathogenicity and ISSR genetic variation.