The genetic relationships between and within some traditionally grown cultivars of olive tree (Olea europaea L.) in Greece (island of Crete) and in Turkey were investigated. Cultivars from Crete included 'Koroneiki', 'Throubolia' and 'Mastoidis', while those from Turkey included 'Samanli' and 'Gemlik'. Cultivars were represented by multiple genotypes of aged trees collected from the field, each one complying with established descriptors. Representative genotypes of wild olive trees from Crete were also employed. A total of 112 genotypes were analysed, employing seven microsatellite (SSR) loci yielding a total of 81 alleles, and reaching a cumulative probability of identity of 6.73 x 10(-09) with a mean observed heterozygosity of 0.852. Analysis of molecular variance significantly partitioned genetic diversity between and within cultivars, albeit with no appreciable difference between the two levels of diversity. All cultivar genotypes aggregated along single, cultivar-specific clusters, pointing to human-driven selection. The two Turkish cultivars 'Samanli' and 'Gemlik' were grouped together. The Cretan cultivar 'Throubolia' grouped together with the two Turkish cultivars, indicating germplasm movement across the Aegean Sea during historical times. Some gene flow was observed between the Cretan cultivars and the native wild populations (likely feral forms). SSR alleles were ranked for their efficiency in discriminating the examined materials, thus establishing a molecular key for cultivar identification. An identification process is proposed including a classification binary tree and provided a method for sorting any new unknown material purportedly originating from any of the analysed cultivars.