Abstract:[Background] Xinjiang is the main producing area of cotton, and Fusarium wilt seriously affects the cotton yield. However, the detailed pathogenesis of cotton Fusarium wilt remains to be reported. [Objective] To select the mutants with reduced pathogenicity from the Fusarium oxysporum mutant library and identity their genes conferring pathogenicity, so as to elucidate the molecular mechanism of the pathogen in causing Fusarium wilt in cotton. [Methods] On the basis of the previously established mutant library of F. oxysporum, By the identification of 136 randomly selected pathogenic mutants. Furthermore, we analyzed the phenotypes and flanking sequences. [Results] we screened out five mutants with significantly reduced pathogenicity, the morphology of mutant B-18 was different from that of the wild type, with purple colonies. The growth rate of the five mutants, especially B-18, decreased. In addition, the five mutants showed reduced spore production. After sequencing of the five mutants, Blast analysis was performed to determine the distribution of T-DNA in the pathogen genome. [Conclusion] From the five mutants with reduced pathogenicity, we identified the genes associated with the pathogenicity. The findings provide a solid theoretical basis for the functional research and cloning of the genes associated with the diseases in cotton.