Post harvest diseases of jujube(Zizyphus jujuba Mill.) fruits are serous problem during storage. Many microbes including benefit and harmful organisms, and pathogens are associated with jujube. The aim of the study was to characterize the microbial diversity in stored jujube fruits and their potential effect on the storage diseases. Microbial diversity of the Ningxia jujube (Zizyphus jujuba Mill.) fruit surface at different mature levels during the harvesting and storage stages was investigated. The jujube maturity was graded based on the percentage of erubescent area of the jujube fruit surface and the tenth grade was with the 100% of the area erubescent and the eighth grade was with 2 third of the area erubescent. The samples were collected at the picking time, and after storages of 15 d, 30 d, and 45 d. The result showed that 80% of the microbes isolated on the jujube surface are bacteria. Fungi including species of Alternaria, Fusarium, Penicillium, Trichoderma, Aspergillus, Mucor and Rhizopus were detected at all sampling stages. Alternaria spp. were the dominant and Fusarium spp. and Trichoderma spp. were common at the picking stage and the storage stages, while species of Alternaria, Penicillium, Trichoderma and Fusarium were dominant and species of Aspergillus, Mucor and Rhizopus were common at the storage stages. The preservative treatment was significantly reduced the fungi colonized on the jujube surface during the storage compared with non-treatment. More microbial diversity was found on the full mature jujubes than that on the eighth grade mature jujubes. Microbial diversity and their effect on the jujube quality were significantly increased along with the time of jujube storage. The biodiversity analysis showed that microbial diverse index of the jujube surface increased during the storage period. The Shannon-Wiener index has increasing tendency for all test treatments and reached to the highest at the storage of 45 d. The Simpson index was significantly inhibited at the picking time and earlier storage stages by the preservative treatment and reached the same as the non-treatment at the storage of 45 d. Although our current result was preliminary, it provided comprehensive understanding on the microbial community of jujube fruits and their effect on the jujube storage diseases. Our performance encouraged that the microbial community of other fruits should be conducted and investigated during storage, and the microbial community function should be determined. The antagonistic microbes may find from the community and are potential in biocontrol of fruit post harvest diseases.