The malformation disease of mango by Fusarium moniliforme var. subglutinan is one of the major causes of huge economical loss every year. Early diagnosis of the pathogens can help cultivators to protect the mango orchid and fruits from successive and secondary infection. The molecular detection is one of the better choices among available techniques for diagnosis. But the farmers or individual cultivars from tropical and subtropical countries like India, Pakistan, Malaysia, Vietnam, Philippines, have lots of limitation to use molecular method. Another problem with this pathogen is lack of specific biomarker. Thus the present study was designed to develop a morphological and histopathological methodology to detect Fusarium moniliforme var. subglutinans and its host-pathogen interaction between fungus and hot tissues. Fresh and preserved (Formaldehyde: Acetic Acid: Alcohol (FAA) solution) tissues were used to check the efficacy of the method. The inter and intracellular distribution of fungal hyphae, in various tissue like cortex, phloem and parenchymatous pith cell, was clearly revealed by this method. The characteristics which were observed like detection of the mycelium threads at the juncture of the shoot tip, axillary buds, petels and sepals axis of the malformed or infected tissues. The Resin accumulation in the parenchymatous and other cells of vegetative tissue was also found as characteristics of this pathogen infection. This study is being also important in terms of identification and growth behavior of the pathogen.