Aetiology of mango malformation (MM) has intrigued the scientists since its inception. The objective of the study was to glean an insight into association of the fungus, Fusarium mangiferae, with different malformed regions, viz. panicle-shoot juncture, apical buds, primary and secondary peduncles, in five exotic mango cultivars. Tissue assays revealed an infection of 88.5, 84.75 and 82.5% in cvs Zill, Sensation and Tommy Atkins, respectively. Least infection of 69.75% was found in cv. Keitt. No exotic cultivar was found to be free of fungal infection. Apical buds proved to be the potential infection site of the fungus amongst the four malformed regions, hosting maximum withintissue infection of 86.2%. Determination of F. mangiferae at proximal and distant sites of the malformed panicles exhibited maximum recovery of 82.0% at 0 cm and only 3% at >30 cm distance beneath the panicle. In the case of non-malformed panicles, an infection of 14.0% was recorded at 0 cm distance while no detection could be made from non-malformed branches. Moreover, examination of ultra-thin bud sections under Transmission Electron Microscopy (TEM) revealed inter-and intra-cellular ramification of fungal hyphae, indicating fungal ingress in malformed bud tissues of local cv. Malda. The present studies explored the sites hosting the causal fungus in mango and provide convincing evidence that F. mangiferae is responsible for turning healthy tissues into the malformed condition. These findings suggest that inoculum specific management strategies are needed in future to curb malformation disease in mango orchards.