Abstract: 【Objective】 The purpose of this study is to investigate the population classification and difference by 6 pairs of gene sequences of the pathogens from Aral City,Ist Oivision,Xinjiang Production and Constraction Corps. 【Methods】 Typical disease samples were collected for purified pathogens by Koch postulates.The total DNA of pathogens was extracted following a standard cetyl-trimethyl ammonium bromide(CTAB) method,subsequently,the ITS,β-tubulin,EF-1α,ACT,LSU,and RBP2 genes were conducted by PCR amplification and DNA sequencing.【Results】 Pathogenic species of korla pear rot in mixed gardens around Alar Valsa mali var.pyri(V.ambiens、Valsa mali ).Species differences are related ro geographical tocation.There are significant differences in pear rot disease isolates between domestic and foreign and foreign countries.EF-1α、ACT、LSU、RBP2 is more able to reflect interspecific differences, and phylogenetic tree has multiple branches,resulting in interspecific differences. 【Conclusion】 The results showed that Valsa mali var.pyri and Valsa sordida were the main diseases in Korla pear.It was clear that the difference existed between the species and population distribution of canker disease pathogen in Korl pear.The main shelterbelt such as poplar is the most common windbreak in Southern Xinjiang,maybe there is a cross infection of fruit trees and wood trees.