Mango is an important fruit crop in Taiwan. Recently, severe fruit rot disease was found frequently on harvested mango fruits. To monitor the incidence of disease and to characterize the causal agent, we performed a field survey in the major mango-producing areas of southern Taiwan, including Guntain, Fanshan, and Yujing, during 2009-2011. The results showed a disease incidence ranging from 18.7% to 58.1%, with those of Guntain significantly greater than the incidence found in Yujing and Fanshan. Based on morphological characteristics and nucleotide sequences of the internal transcribed spacer (ITS), beta-tubulin gene (TUB) and elongation factor 1-alpha (EF1-alpha) gene, we identified four Botryosphaeriaceae species, including Fusicoccum aesculi, Neofusicoccum mangiferae, N. parvum, and Lasiodiplodia theobromae. Pathogenicity tests indicated that all of these fungal species were pathogenic to harvested mango fruits, and L. theobromae was the most aggressive pathogen. Moreover, when attached, immature mango fruits were inoculated with conidia of Botryosphaeriaceae species, disease symptoms characteristic of fruit rot appeared on the fruits after harvest and ripening. These findings indicated that L. theobromae, F aesculi, N. mangiferae, and N. parvum were all causal agents of the new fruit rot of mango. Furthermore, their conidia may serve as important sources of inocula causing fruit rot disease in mango orchards.