Pomegranate (Punica granatum L.) is an important fruit species for Turkey where many cultivars are being cultivated. In this study, we determined the fruit characteristics and RAPD band patterns of six local cultivars from Hatay, Turkey. Our results demonstrated that there is a great level of morphological variation. The principle component analysis of 18 quantitative fruit characteristics revealed that fruit weight, aril number/fruit, peel color and soluble solids/acidity ratio are important traits for discriminating the cultivars tested. The UPGMA cluster of fruit characteristics indicated that 'Katirbasi' and 'Kan nari' were similar to each other and they were separated from rest of the cultivars. Twenty-two RAPD primers generated total of 106 reproducible bands 22% of which were polymorphic. The UPGMA dendrogram of RAPD data showed that 'Tatli nar' and 'Serife' were very closely related while 'incekabuk' is distinct from the other cultivars. As a result, discrepancies were detected between morphological and molecular data. Therefore, we confirmed that diversity among the fruit characteristics were not good indication of genetic relatedness while molecular tools are valuable to study such similarities.