Papaya is a prevalent and economically vital fruit tree that comprises of several varieties worldwide. Basically, four varieties of papaya cultivated in Odisha namely Coorg Green, Washington, Honey Dew and Ranchi selection were analyzed at the morphological and the molecular level in order to understand their genetic diversity. Morphological characters applied for the comparison of species included the mature papaya leaves, inflorescences, petioles and fruits. For this molecular study, genomic DNA was amplified using the RAPD-PCR reaction. This RAPD primers yielded adequate polymorphic bands revealing variances between the papaya varieties with which a dendrogram was made.