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Genus Momordica, is widely distributed over tropic and sub-tropic region. Besides the cultivated bitter gourd (M. charantia L. var charantia), many other species of the genus occurring in the wild state have been found in India and neighboring countries. Among them, monoecious, M. charantia and M. balsamina and dioecious, M. dioica and M. cochinchinensis exhibit divergence in morphological characters like growth habit, maturity, and fruit shape and size, sex expression, leaf, root and seed charactersThe analysis of study based on dendrogram obtained from the distance matrix from the mean value of the 15 quantitative traits for the genotypes grouped all the accessions into two major clusters. One cluster separates two distinct groups each accessions of M. charantia and M. cochinchinensis and M. balsamina formed distinct group within a major cluster while the second major cluster consisted of all accession of M. dioica. For molecular diversity analysis, 101 primers including 50 RAPD, 16 SSR and 35 ISSR primers produced a total of 600 scorable amplicons across four species, of which 586 (97.08%) were polymorphic. Seventeen markers differentiating monoecious and dioecious and 85-amplicons specific to one of the four Momordica species were identified. The UPGMA dendrogram obtained from Jaccard’s similarity coefficient (average similarity of 0.38) showed two major clusters clearly distinguishing monoecious and diocious species with high bootstrap value (100) between nodes.Not Availabl