Abstract: 【Objective】 To find out whether there is a cross infection of rot pathogens in different hosts of orchard in Xinjiang in a micro-ecological environment. 【Method】Using the apple (M. pumila Mill), Xinjiang Populus bolleana and Pyrus sinkiangensis rot disease materials in the fifth Regimental Farm of Aksu prefecture of Xinjiang as the experimental material, the cross infection experiment was carried out by the shoot inoculation method; The tubulin and EF-1α gene sequences were constructed by Neighbor-joining (NJ) to analyze the phylogenetic tree. (M.pumila Mill)、(Populus bolleana)(Pyrus sinkiangensis)Using β-tubulin and EF-1 α gene sequences, the corresponding sequences of homologous genes were queried in NCBI database, and then the phylogenetic tree was constructed by neighbor-joining (NJ) method, and the sequence analysis was carried out. (Neighbor-joining,NJ)。【Result】The results of cross-infection showed that the rot pathogens of different host sources could infect each other between apple, Xinjiang poplar and Korla pear. Among them, the rot pathogens derived from pears were the earliest, followed by the rot pathogens originating from Xinjiang poplar; Those originated from apple rot pathogens had the latest onset. Sequence analysis of the β-tubulin and EF-1α genes revealed that the three different host-derived rot pathogens were grouped together. The host of the homologous sequence derived from the apple rot pathogen was apple. Hosts derived from the homologous sequences of Xinjiang poplar are apples and pears. The host of the homologous sequence derived from Korla pear rot pathogen was poplar. 【Conclusion】There existed am cross infection between apple, fragrant pear and poplar in Xinjiang orchard in microecological environment.