Abstract: The objective of this project was to clarify the main pathogenic fungus on harvested Akesu Fuji apple after rotten.The harvested Akesu Fuji apple was used for the isolation and screening of pathogenic bacteria under the condition of room temperature and low temperature.The method was the classical microorganism of isolation and screening with the morphological observation,the internal transcribed spacer,( ITS) 28 S ribosomal( large subunit r DNA,r DNA- LSU) and testing the sequence of microtubulin B( Beta tubulin,β- tubulin) as well as the structure of phylogenetic tree.Meanwhile the verification of tie- back of bacterial strain and the lesion were conducted.The lesion was separated into two fungus from the storage of red Fuji apple,and also the two fungus were identified as Alternaria sp.and Penicillium sp.through the morphological observation.Further sequence analysis using the tie- back of bacterial train and lesion confirmed that,the two types of Fuji were Alternaria alternata and Penicillium expansum.This study provided the theoretical basis for the research of rapid identification of pathogenic bacteria in harvested Akesu red Fuji apple in Xinjiang.