Numerous olive cultivars are cultivated in Iran, mainly in the north. Ninety-two accessions belonging to 10 main olive cultivars were screened by 13 microsatellite markers revealing high genetic variability both within and between cultivars. In total, 72 alleles were detected with a mean number of 5.5 alleles per locus. Twenty-four unique allelic patterns were observed, whereas six genotypes showed 15 unique alleles. Heterozygosity ranged from 0.00 to 0.98, whereas the mean number of discrimination power and polymorphic information content were 0.55 and 0.54, respectively. The combination of 5 simple sequence repeat markers made discrimination of 84% of all accessions included in the study possible. The existence of homonyms, synonyms, or mislabeling as well as intracultivar polymorphism was revealed by allele differences between accessions of the same denomination. The phenogram showed variability among as well as between some cultivars, but most accessions with the same generic names were grouped together.