Apple ( Malus sp . ) is consider one of the world’s most grown fruit trees and has the forth place after citruses, grape and banana and it is one of the common pomes fruit planted in the temperate regions. Iran is one of the major apple producers in the world and it locates near the original place of apples. Beside well known cultivars, introduced from other countries, many traditional genotypes are cultivated in wide range in different provinces of Iran . Among these local genotypes, there is a group of apples named as, Golab apples, which appears particularly interesting for their high quality, early ripening, special aroma and taste. Despite high richness in genetic diversity of Golab apples, little is known regarding the genetic relationships among native apple genotypes of Iran . Therefore, the objectives of this study were based on determining genetic variations among Golab apples and other introduced commercial cultivars of apples in Iran using Simple Sequence Repeat (SSR) and Inter Simple Sequence Repeat (ISSR) markers. In this study, Genetic diversity of 27 apple genotypes was assessed using 22 pairs of SSR primers that generated between three to 11 alleles with average of 5.4 alleles per primer and it showed high (0/976) heterozygosis. The cultivars were divided in to five sub-clusters. Based on the SSR dendrogram using Power marker software, clear-cut separation was found between Iranian apples and imported cultivars. None Iranian cultivars with one local apples, Ahar-2, were grouped together, whereas Iranian genotypes jointly with Golab genotype were Isfahan with Golab- e Janaty, Golab Sahneh and Damavand showed the highest similarity than other tested genotypes. Twenty ISSR primers were screened that yielded the total of 202 (83.1%) polymorphic bands. The dendrogram derived from ISSR data clustered the accessions in four major groups, confirming the associations between Golab apple genotypes. Over all clustering these apples together in the same groups in the both methods confirmed the hypothesis that all Iranian Golab apples which have same morphological traits may belong to one germplast and over the years they have distributed in different areas. The results showed that the Iranian Golab apple cultivars have closer affinity with each other than other cultivars. These results suggest that ISSR and particularly SSR markers have higher level of discrimination in evaluating genetic diversity and fingerprinting of apple genotypes
