Molecular markers have been used for genetic study and identification of cultivars belonging to different fruit species for a long time. In this study ISSR, RAPD and SSR markers were used to evaluate genetic variation and relationships among 95 apricot and one plumcot cultivar located in the Apricot Germplasm Repository in Malatya, Turkey. All three marker systems distinguished the apricots in various levels. The highest polymorphism (98%) was obtained with simple sequence repeat (SSR), followed by inter-simple sequence repeat (ISSR) (88%) and randomly amplified polimorfic DNA (RAPD) markers (77%). The similarity values were between 0.49 and 0.94 among apricot cultivars. ‘Sekerpare Igdir’ and ‘Sekerpare Benzeri’ were the most similar (0.94). The UPGMA dendrogram constructed using combined data of three marker systems separated the genotypes into two main clusters: one cluster included genotypes originating from Malatya and the other regions, and the second cluster contained cultivars mostly from Mediterranean region. The plumcot cv. ‘Kayisi Erigi’ was outgroup. These results supported that apricots in Turkey indicated considerable genetic diversity.