Bitter gourd (Momordica charantia L.) is known tropical cucurbitaceous vegetable for its nutritional, medicinal and curative properties. The immature fruit is valued for its bitter taste and richness in calcium, phosphorous, iron, copper, potassium and vitamins A, B1, B2 and C. The genus Momordica consist of 60 species worldwide and out of them 7 species (Momordica charantia, M. balsamina, M. dioica, M. cochinchinensis, M. tuberosa, M. subangulata M. macrophylla) are found in Indian sub-continent which expressed large variability with respect to fruit shape, size, coulour due to varied edaphic and climatic conditions. Breeding efforts for emergence of early pistillate flower at earlier nodes, high female to male sex ratio, earliness, fruit color, firm fruit with narrow seed cavity, less seed development, desirable fruit shape, size, non-ridge fruits, thick flesh, thick flesh, resistant to leaf mosaic and fruit fly and suitability for export, canning and dehydration. Considering the above traits, several varieties and hybrids in different segments has been developed by public and private seed companies. Due to monoecism and expression of gynoecism has played a vital role in development of high yielding varieties, hybrids and seed production. The major limitations of molecular markers are limited in number, and their association with few economically important traits in bitter gourd. Generation of high-density genetic maps is the best way to identify the closely associated or functional markers for marker assisted selection and map-based cloning for fruit-related traits, gynoecium sex and yield. Crop wild relative can play an important role as a source of stress tolerance. The availability of whole genome information, selection of biotic and abiotic stress tolerant genes along with heterosis related alleles can be easily accomplished in breeding programmes.