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A total of 111 accessions belonging to 60 olive cultivars, and one accession of oleaster, native to Italy, Spain, France and Greece, have been screened with three AFLP primer combinations and 27 microsatellite primer pairs in order to characterise their genotypes and reveal their genetic relationships. A total of 70 AFLP and 80 SSR polymorphic bands were scored. Comparisons were made between AFLP and SSR marker variability, efficiency and usefulness for genetic relationships and cultivar identification. The data obtained were analysed using the Jaccard genetic similarity coefficient, applying the SAHN clustering method. A dendrogram of genetic distances was produced. All genotypes studied could be distinguished unequivocally using a combination of SSR and AFLP markers. Cultivars were grouped into three clusters according to their type of use: oil, table, or dual purpose cultivars.