Abstract: 【Objective】 Based on the observation of the characteristics of pathogen culture, combined with molecular biology technology, to determine the species and related relationship of apple tree rot fungus in Aksu area in the hope of providing theoretical basis for effective control of apple canker. 【Methods】 The pure culture of Apple Tree Valsa Canker was obtained by Koch's Rule. The morphology and culture characters were observed and recorded. The DNA of the strain was extracted by improved CTAB method and then sequenced. After sequencing, the blast homology was compared and analyzed on NCBI website. Then the β - tubulin and EF1 - α sequences were analyzed by adjacency method and after that, phylogenetic tree was constructed. 【Results】 The optimum temperature for mycelium growth was 20-30℃, the optimum PH value was 5-6, and the optimum carbon and nitrogen sources were glucose and peptone; A total of 11 strains were isolated. The strain could be inoculated on healthy apple branches and the same strains could be isolated. It turned out that each strain was closely related to Valsa Mali, Valsa ceratosperma. 【Conclusion】 The apple tree rotting bacteria in Aksu area are V. Mali (asexual C. Mali) and V. ceratosperma (asexual C. sacculus), among which, V. Mali is the main pathogenic species. There are different types of culture characters on PDA.