Apple ( Malus domestica Borkh, Rosaceous) is forth produced fruit in the world after orange, grape, and banana, respectively and is considered as the most important fruit in the temperate regions. From the commercial point of view, Iran is forth producer country and the seventeenth apple exporter country in the world. This plant is highly diverse because of being nearly apple , s center of diversity and the cultivation of the plant in different regions of Iran. Most of Iranian apple cultivars have called according local names; so their genetic relations aren't so specified. Here in order to determine genetic diversity of various Iranian apple genotypes and comparison between their genetic relations with commercial cultivars, we used microsatellite and SRAP markers in 68 apple cultivars. Among 14 used microsatellite primer pairs; 9 of them were polymorphic with the number of amplified alleles from 4 to 9. The average number of alleles and heterozygosity for all the loci were 6.22 and 0.808, respectively. UPGMA dendogram of microsatellite data constructed by Nei's similarity coefficient and using Power marker v.3.25 software divided the genotypes in five sub-cluster including two external groups with the exception of Wealthy and starking-2 and three group of Iranian apples. Among 56 SRAP primer combinations, 13 of them were polymorphic and produced 194 polymorphic bands. The band patterns of SRAP marker was analyzed by Jaccard's similarity coefficient and UPGMA method and using NTSYS pc 2.02 software. In this dendogram, most of the genotypes (94.1%) set in first sub-cluster. The Imperial All Red cultivar was set in group 2 and three Iranian genotypes, Asalli, Golbahar, and Mashhad jam, apart from other Iranian cultivars were grouped in sub-cluster 3. The average of, heterozygosity was computed 0.3390 that seems not to be logical, because apple is an self-incompatible plant, whereas, the average of heterozygosity microsatellite marker was 0.808, which confirmed the self-incompatibility of apple. The results revealed that the microsatellite marker is more reliable than SRAP marker for indicate information of polymorphic and amount of heterozygosity in apple genotypes. Because the microsatellite markers are codominant and SRAP ones mostly are studied dominant, therefore, microsatellite markers are able to separate the heterozygote and homozygote genotypes, whereas, SRAP markers amplified different loci in the genome and the data scored by 0 and 1 as a dominant marker it could not able to precisely separate heterozygote and homozygote genotypes. Key Words: Apple، Genetic diversity ، SRAP، Microsatellite