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To study pomegranate genetic variation in Kermanshah province, 44 pomegranate samples were collected from six different regions. In overall 48 morphologic traits were evaluated. Cluster analysis based on morphological traits grouped samples in four clusters. To study pomegranate genetic variation in molecular level, RAPD and ISSR markers were used. Totally 183 bands were amplified by 20 RAPD primers, 94 of them were polymorphic with average polymorphism percentage of 51.37. Cluster analysis arranged samples in 7 clusters which often were conformed to morphologic results. Coffenetic coefficient was 0.996. An overall 114 bands were produced by 17 ISSR primers, among them 43 bands were polymorphic with average percent polymorphism of 37.71. Cluster analysis arranged samples in 7 clusters which often were conformed to the result of morphologic and RAPD analysis. This research determined the genetic situation of pomegranates and showed that different genotypes were placed in different groups. Results of present research showed that Kermanshah province is a major genetic resource of pomegranate. The results can support the ideas that Iran is motherland of pomegranate.