Muskmelon, which is an important cucurbit of the tropical and subtropical region of the world, shows great diversity, with six different botanical or horticultural groups and fifteen varietal groups. In this study, a total of fifty (50) simple sequence repeat (SSR) markers were used to investigate the genetic diversity and population structure of 46 muskmelon accessions of different horticultural or varietal groups. Thirty-eight (38) of the fifty SSR markers were highly polymorphic. A total of 99 alleles were generated by the polymorphic markers, with an average of 2.06 alleles per loci. Heterozygosity among accessions for individual loci varied from 0.00 to 0.21, with the highest (0.21) reported for the CMCTN71 marker. The gene diversity and polymorphism information content (PIC) values varied between 0.08 to 0.72 and 0.07 to 0.67, with an average of 0.47 and 0.38, respectively. The primer that showed the highest gene diversity and PIC values was DM0913. The unweighted pair-group method for arithmetic average (UPGMA)-based dendrogram classified all the 46 accessions into two major clusters. Population structure analysis classified 46 muskmelon accessions into 2 subpopulations. The subpopulation I contained 29 accessions from the cantalupensis group, and subpopulation II contained 17 accessions from momordica, inodorus and conomon groups, respectively. Analysis of variance indicated that 18 and 68% of variance was due to subpopulations and differences among individuals, respectively. The present study supports the existence of sufficient variation among musk melon genetic resources in India, and their classification based on molecular markers will be helpful to accelerate the breeding programme for specific traits.