Latent infections of mango stem end rot pathogens were investigated in the trees and fruits of two mango cultivars grown in the mango orchard of Guangxi University at different periods. The results of investigation indicated that some stem end rot pathogens were found to occur endophytically in the shoot prior to flowering. There were at least 10 kinds of fungi causing mango fruit rot that obtained from the period of pre-flowering to post-harvest. Except 9 fungi producing conidia, all of the others belonged to nonsporulating fungi. Among the 9 isolated fungi, Dothiorella dominicana Pet.et Cif, Botryodiplodia theobromae Pat. And Diplodina sp.were the major pathogens that caused mango stem rot in the orchard, while Pestalotiopsis mangiferae (P.Henn.) Sutton. and Phomopsis mangiferae Ahmad were the minor ones. D. dominicana., B. theobromae and P. mangiferae latently infected the shoots perior to flowering, Diplodina sp. invaded fruitlets and made ripe fruits rotten. P. mangiferae latently infected ripeless fruits before harvest.