Melon is one of the most important horticultural crops in Iran. There are a few studies on the genetic structure of Iranian melon. A set of 18 simple sequence repeat (SSR) primer pairs were used to assess the genetic diversity in a collection of 24 melon accessions representing different botanical groups of Iranian cultivated melons (vars. inodorus, cantalupensis and dudaim), along with 28 reference accessions from diverse geographic origin. All studied SSR loci were polymorphic that confirmed their usefulness for genetic analysis of melons. A total number of 141 alleles were detected, with an average of 7.8 alleles per locus for reference genotypes and 4.38 alleles per locus for Iranian accessions. The low variability within Iranian melon accessions is reflected by the low values of the observed heterozygosity (with an average of 0.119), indicating lack of intercrossing between accessions or a high rate of self-pollination. Values of observed homozygosity for ''Suski-e-Sabz'' and ''Khatouni'', as the most cultivated melon in Iran, were 0.98 and 0.99, respectively. Cluster analysis divided Iranian accessions into two major groups. The highest level of polymorphism was detected among the dudaim group. The analysis of molecular variance indicated that the majority of variation (87 %) was due to the difference within accessions. The average pairwise genetic distance among Iranian accessions was 0.674.Our results showed a distinct separation of dudaim group from the rest of Iranian accessions, even separated two different groups of var. dudaim with different traits. There was a wide genetic distance between Honey Dew, as the most popular member of inodorus group worldwide and ''Khatouni'', a major Iranian winter melon (GD = 0.809). This genetic distance shows the importance of Iranian accessions for conservation and use in breeding programs.