Molecular markers are widely used tools in genotypic diversity analysis and species identification. Molecular diversity was performed with 15 RAPD primers among 18 diverse accessions (9 drought tolerant and 9 susceptible) of muskmelon. Out of fifteen ten RAPD primers produced 45 amplified DNA fragments ranging in size from 200–2000 base pairs, from which 38 fragments were polymorphic (83.33%) with an average of 4.5 fragments per primer. Six primers were found to be highly informative as they gave unique bands to differentiate between drought susceptible and drought tolerant genotypes. From RAPD profiles similarity matrix was obtained and Jaccard's Similarity Coefficient was observed in between 0.45 to 0.86 and on this basis a dendogram was constructed with UPGMA method. This study demonstrates that RAPD are highly useful for finding markers associated with major and minor genes controlling agronomically important traits in muskmelon.