The interspecific variability of fatty acid (FA) composition and RAPD profiles was used to examine biochemical and genetic relationships among six pomegranate cultivars, which dominate pomegranate production in Southern Anatolia Region of Turkey. Fatty acid composition of pomegranate leaves was determined by using gas chromatography. Differences in the FA composition were found among cultivars. In particular, cv. kirli hanim had a distinct fatty acid profile that differs from the other cultivars. Linoleic acid was not detected in this cultivar, whereas the other cultivars had various levels of linoleic acid. RAPD data also showed that this cultivar formed a unique pattern. The differences in the composition of fatty acids among pomegranate cultivars suggested that fatty acid profiles could be used to differentiate among some of the pomegranate cultivars. RAPD analysis was also useful for grouping the pomegranate cultivars. (C) 2007 Elsevier Ltd. All rights reserved.