Jujube fruit is thin-skinned, thick flesh, tender and juicy. During post-harvest transportation, jujube fruit is vulnerable to be damaged and infected by microorganism. In this study, pathogenic fungi that caused postharvest rot and deterioration of jujube were isolated from the infected jujube fruit. Based on morphological observations, fungal rDNA internal transcribed spacer (ITS) sequence analysis, the phylogenetic tree was constructed. Meanwhile healthy jujube fruit was re-inoculated with all of the purified isolates and symptom of lesion was verified. Three filamentous fungi (221^# , 227^# and 232^# ) were isolated from natural infected winter jujube during post-harvest storage and two filamentous fungi (229^# and 230^# ) from jun jujube fruit. According to the morphological observation, the genus of the five fungi strains belong to Fusarium (221^# and 227^# ), Stemphylium (229^# and 232^# ) and Aureobasidium (230^# ). The results obtained by the analysis of rDNA ITS sequence of five strains were identified as 221^# (Fusarium equiseti), 227^# (Fusarium incarnatum), 229^# (Stemphylium lycopersici), 230^# (Aureobasidium proteae) and 232^# (Stemphylium armeriae) respectively. None of these five pathogenic fungi strains had been reported to cause postharvest diseases of jujube, among which S. armeriae was not reported to cause plant diseases. The study aimed to discover more pathogenic fungi species causing jujube diseases, and hoped to provide a theoretical basis for biocontrol measures for jujube fruit diseases.