BACKGROUND: Bitter gourd (Momordica charantia L.) is an important vegetable crop in tropical countries, including China and India. A wide range of genetic diversity exists in India with respect to fruit morphology such as colour, size and exocarp. A diversity assessment conducted using different DNA marker systems amplified fragment length polymorphism (AFLP), inter simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) markers) will be helpful in the establishment of a broad-based description for improved germplasm curation and the identification of germplasm for genome mapping and breeding of bitter gourd.