In the present study, a total of 142 fungal strains were isolated from 180 samples of the leaf, stem and bark tissues of sacred tree Couroupita guianensis from an unusual semi-arid tropical region. The tissues of the samples were grown in potato dextrose agar (PDA) medium and the endophytic mycoflora were identified based on the morphological characteristics. Among all the strains, 130 were fertile, which belong to 11 species and 12 sterile morpho species. The relative frequency of isolated individual endophytic fungal group consists of hyphomycetes (41.5%), coelomycetes (32.4%), ascomycetes (13.4%), zygomycetes (4.2%) and sterile fungi (8.5%). Among the fungal isolates, Scytalidium acidophilum and Mycosphaerella sp. were recorded as the most dominant fungal isolates in the leaf tissues, Cladosporium cladosporioides and Colletotrichum falcatum were observed as the dominant endophytic fungal isolates in the stem tissues and Botryodiplodia theobromae was found to be predominant species in bark tissues of C. guianensis. The species of Colletotrichum were found only in stem tissues. Therefore, the endophytic mycodiversity were high and abundant and they were distinctly associated with host plant. All statistical analyses confirmed that leaf tissues contained more endophytes than the stem and bark while Colletotrichum exhibited organ specificity. The present study revealed that the sacred tree C. guianensis is one of the ecological niches for sheltering endophytic mycoflora eventhough in harsh climatic conditions.