Abstract: To study the genetic diversity of the melon collection at the National Plant Genetic of Iran, 35 genotypes were planted at Bu Ali Sina University Hamedan in 2004 and were evaluated with 15 micro satellite SSR markers. Micro satellite markers in the upper levels showed polymorphisms and 87% of them are polymorphic and 63 alleles have been identified. The number of effective alleles in the polymorphic loci varied from 1.25-8.19 and the mean is 2.80. The percentage of genetic loci having polymorphism is 87.67%. Cluster analysis of genotypes was divided into 5 groups wherein genotype of foreign origin has smooth skin while different groups of Iran genotype are netted. Genetic distance between Iranian and foreign is 0.98. Results obtained from this study showed the significant difference between Iranian genotypes with other genotypes. These genotypes have high diversity which could be used in breeding programs.