Abstract:[Background] Sweet cherries are highly perishable fruits because of their tender and juicy flesh. Shihezi is one of the newly plantation area of sweet cherry in Xinjiang, however, the economic losses caused by postharvest rot are huge. [Objective] In order to improve the postharvest quality and prolong shelf life of sweet cherry, this study aims to isolate and identify the pathogens from sweet cherry harvested in Shihezi. [Methods] Fungal strains were isolated from decayed sweet cherry harvested from 136 regiment, Shihezi, and these strains were inoculated back to healthy sweet cherry to test the pathogenicity according to the Koch’s postulates. Pathogens were identified using morphological characteristics and internal transcribed spacer (ITS) sequences analysis. [Results] Five types of filamentous fungi were isolated from the rotten tissue of sweet cherry, in which three types were pathogens of sweet cherry fruit harvested in Shihezi. The representative strains were identified by internal transcribed spacer sequences as Mucor fragilis, Fusarium sp. and Penicillium camemberti, respectively. [Conclusion] M. fragilis, Fusarium sp. and P. camemberti were pathogens causing postharvest rot on sweet cherry harvested in Shihezi, Xinjiang.