Quince tree ( Cydonia oblonga Mill.) as an individual species of this genus is one of the several kinds of pome fruits. Although it's genuine origin has been unknown but it can be suggested that Iran, Middle Asia, Anatolia and Greece are as their probable origin rather than others. This plant belongs to subfamily of Maloideae and family of Rosaceae . For the first time in this research the genetic relationships of quince genotypes in Iran where is one of the possible origin has been studied. In year 2007, Turkey has been known as the greatest quince producer in the world. In year 2005, the quince cultivated plane in 26 provinces of the country is 5804/57 hectares and its quantity production has been estimated to be 39312/98 tons. Isfahan has been shown as the greatest quince producer in Iran. Following Isfahan, Fars, Kerman and Razavi Khorasan provinces have been ranked as the greatest quince producers of this product. Having various ecological conditions, Iran from the remote past had been suitable slaughter house for this plant. For the present time, there are not found any precise information about the genetic relationships of the quince genotypes in Iran and foreign varieties in the world. In this study, 20 genotypes were belonging to Isfahan and Razavi Khorasan provinces and three foreign root stocks including quince A, B and C was employed. Two methods on microsatellites including SSR (Simple sequence repeat) and ISSR )Inter simple sequence repeat) was conducted in order to determine their genetic relationships. Because lack of any the special primers of this plant, therefore 28 pairs of apple SSR primers have been used and amonge which the eight pairs of SSR have been shown with cross- genus amplification and 10 loci middling produced 2/8 alleles. The SSR markers dendrogram was obtained through using coefficient of Nei (1983) and method of UPGMA by Power marker software showed that the used genotypes in this research can be divided into Isfahan province's genotypes and Razavi Khorasan's ones, and the three root stocks used were set in the group of Razavi Khorasan province's genotypes, and those have shown the genetic affinity with respect to these genotypes. The quince A with Neishaboor- Deezbad with zero genetic distance was settled in one group. Consequently, the quince B having a little difference has shown a close relationship to quince A, and it in company with Torbate jam genotype was set in one group. Quince C was alone set independently in the group of Razavi Khorasan province's genotypes. It seems as though that in the group of Razavi Khorasan province's genotypes, two genotypes of Neishaboor- borj and Neishaboor- kharv are probable origins of two groups of Razavi Khorasan genotypes. In the group of Isfahan provinc
