The aim of the study is to determine genetic diversity and relationships among olive cultivars native to Croatia and Turkey. A total of twenty olive (Olea europaea L.) cultivars including fourteen from Croatia and six common cultivars from Turkey were analyzed for genetic diversity and relationships by using six microsatellite markers (DCA05, DCA09, DCA18, GAPU71B, GAPU101, UDO43). The number of polymorphic alleles ranged from 2 (UDO43) to 5 (DCA09), with an average of 3.6 fragments per marker. UPGMA cluster analysis based on simple matching similarity matrix grouped cultivars into three main clusters. Two pairs of cultivars from Croatia ("Buža muška" and "Levantinka"; "VLMD6" and "Drobnica") were thought to be different, although they produced identical SSR profiles. Cluster analysis points to some genetic relationships between Croatian and Turkish olive cultivars. The results also indicate efficiency of SSR markers to evaluate genetic diversity in olive and identify misnamed or synonym individuals.