Sweet cherry ( Prunus avium L., Rosaceae, 2 n = 16) is cultivated in temperate regions of the world for its edible fruit. Iran is one of the three biggest cherry producer after US and Turkey in the world. Annual production of all kinds of cherry in Iran exceeded 200000 tons (FAO). In recent years a great research has been conducted on sweet cherry and sour cherry breeding specially on their rootstocks with aims to introduce dwarf and compatible ones. All commercially grown sweet cherries use a rootstock in combination with a grafted or budded scion variety. Rootstocks can directly influence productivity, precocity, tree size, tree architecture, fruit size, and fruit quality. The choice of certain rootstocks will also influence many horticultural decisions such as pruning, training, tree support, and labor management. Mazard ( Prunus avium) , Colt, Sour cherry ( Prunus cerasus) and Mahaleb ( Prunus mahaleb) are used as a common rootstock for sweet cherry in the world. The best cherry rootstock for Iranian nurseries and orchards is Prunus mahaleb Mahaleb has been known as a cultivar with strong roots which grows as well as tolerant plants in poor and dry soil such as soil with iron and zinc deficiency. Mahaleb demonstrates a cold tolerance trait and can endure temperatures as low as -20 ? C, so it can be a suitable rootstock for climate of Iran. However Iran has a wide spectrum of Mahaleb’s genetic diversity but the phylogenic information of Iranian accession are not available. Therefore, this study has been done with aims to evaluate genetic variation of Mahaleb germplasms which collected at the Horticultural Department of Mashhad, Iran. Owing to have a little special primers of this plant, In this study genetic variation of 60 Mahaleb genotypes was assessed by using 9 pairs of sweet cherry, 4 pairs sour cherry and two pairs of peach SSR primers. Ten out of fifteen primers demonstrated two to five alleles with an average of 2.11 alleles per primer and it showed 0.4 heterozygosity and average of polymorphism information content(PIC) was 0.46. The SSR markers dendrogram has been illustrated by power marker software with coefficient Nei(1983) and the Neighbor-joining method. Analysis of SSR data clustered the mahaleb genotypes into six group. The third group has 15 genotypes. The 7 of 15 accessions were dwarf and late flowered. Thirteen out of thirty-one ISSR markers have been tested and produced 40 polymorphic band. ISSR data were used to illustrate dendrogram in NTSYS V. Pc-2.02e by using Jaccards similarity coefficient and Neighbor-joining method. The result demonstrate that Mahaleb genotypes have been divided into seven groups. ISSR’s demdrogram in contrast with SSR’s dendrogram showed no relation between morphological characters. The result demonstrate that ISSR marker are hardly able to show genetic