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This study aimed at identifying fungal pathogens causing pre‐ and postharvest fruit rots on local cultivars of mango (Mangifera indica L.) in the main mango‐growing regions of southern Iran. Mango fruits showing rot symptoms from commercial orchards were used for isolation of fungal species associated with preharvest fruit rots. Latent infections were assessed on intact healthy mango fruits which were surface‐disinfested and incubated in moist chambers at 25ºC. For evaluation of postharvest wound infections, intact healthy mango fruits were artificially wounded and incubated in moist chambers at 25ºC. In addition, fungal decays were assessed on intact healthy mango fruits stored at 13ºC for up to 4 weeks. Isolated fungi were identified based on morphological characteristics, as well as sequence data from the ribosomal internal transcribed spacer (ITS) region. In addition, the sequence data inferred from translation elongation factor 1‐alpha (tef1) gene were used for determination of Fusarium species and Alternaria and Colletotrichum isolates were defined genetically based on multi‐gene sequencing. Accordingly, eight fungal species, including Alternaria alternata, Neofussicoccum mediterraneum, Aureobasidium melanogenum, Colletotrichum gloeosporioides, Fusarium proliferatum, Xenoacremonium falcatus, F. verticillioides and Diaporthe phyllanthicola, were identified to associate with preharvest mango fruit rots. Fungi associated with latent infections, mostly stem‐end rots, included A. alternata, N. mediterraneum, C. gloeosporioides, Lasiodiplodia theobromae, F. proliferatum and A. melanogenum, and those associated with wound infections were A. alternata, N. mediterraneum, Penicillium spp. and Cladosporium spp. A. alternata was the only pathogen isolated from the fruits stored at low temperature. Pathogenicity of the selected isolates was demonstrated by fulfilling Koch's postulates.