Abstract: This study is aimed to investigate the genetic variation and pathogenic differentiation of cotton verticillium wilt in Shihezi region of Xinjiang. By the microscopic observation of isolates，the cloning of ITS sequences and the construction of molecular phylogenetic tree，the isolation and identification as well as pathogenicity of various cotton verticillium wilt from different hosts were analyzed. The results showed that the isolated 24 strains of cotton verticillium wilt all belonged to Verticillium dahliae，of which 11 strains were deciduous cotton verticillium wilt and the rest were non-deciduous cotton verticillium wilt. The results of molecular phylogenetic tree showed that 24 strains belonged to two different branches. The infection results to the same host showed that the pathogenicity of 24 strains was classified into three types：strong，moderate，and weak. The strong one was 75%，and it was 23.3% higher than that of 51.7% in 2010，indicating that the pathogenicity types of cotton verticillium wilt in Shihezi region changed greatly and more virulent strains appeared；this probably was correlated with many years planting cotton in Shihezi region. Among them，SHZ-9 was the most virulent while SHZ-4 was the weakest pathogenic strain，indicating that there was obvious pathogenic differentiation of cotton verticillium wilt in Shihezi region. In conclusion，the different virulence strains could be divided into three nutrient affinity groups（VCGs）. The results of this study demonstrated that the pathogen of cotton verticillium wilt in Shihezi region of Xinjiang was Verticillium dahliae，the strong virulence strains increased and the genetic differentiation of strains was significantly different.

Key words: cotton verticillium wilt, molecular phylogenetic tree, pathogenicity