Abstract: 【Objective】 To identify morphological characteristics and pathogenicity of cotton Verticillium wilt collected from Changji and Shawan in the hope of comprehending the pathogenicity and differentiation of the cotton disease in northern Xinjiang. 【Methods】 The molecular detections of the pathogenicity for cotton wilt disease were performed using specific primers DB19f/DB22r for defioating pathotype and INTND2f/INTND2r for nondefioating pathotype. Whole genome resequencing was performed using SNP loci as markers for genetic diversity analysis. The colony morphology and the pathogenicity were identified adopting the virulence strain V991 as the control, chlorophyll fluorescence imaging technology was employed to compare and observe the disease changes and the trend of fluorescence parameters of Vd-3 and V991. 【Results】 Molecular identification showed that all 14 strains examined were defioating pathotype. In comparison with V991 strain, Vd-3 exhibited the highest disease index and high pathogenicity with different infection modes and rapid infection rates; The infection of Vd-3 was seen that the disease symptom extended from the leaf margin to the center, while the that of V991 spread from the sporadic distribution of the mesophyll to the leaf margin and then to the central part by observing the dynamic changes of imaging and fluorescence parameters employing the chlorophyll fluorescence imaging system. The daily variation trend of fluorescence imaging and parameters infected by Vd-3 plants was more obvious; The quantum yield Y (NO) of non-regulatory energy dissipation and the non-photochemical quenching (NPQ) reached the inflection point on the 6th day. The maximum photochemical quantum yield (Fv/Fm) and the actual optical quantum yield Y (Ⅱ) changed slowly, and the Fv/Fm showed obvious difference at 13 d. 【Conclusion】 The strains from Changji and Shawan city are defioating pathotype, and the colony is circular with 2 hyphal branches and long oval spores. In addition to the greatest genetic distance and variability, the most virulent strain of Verticillium wilt disease is Vd-3. Compared with that of V991,Vd-3 possesses the varied the infection mode for cotton, and fluorescence parameters Y (NO) and NPQ can exquisitely perceive the changes.