In this study, the genetic variability and relationships among wild and cultivated pomegranate genotypes from the north of Iran were investigated by morphological characters and RAPD molecular markers. Principal component analysis showed that the first three components explained 61.64 % of the total morphological variation for studied genotypes. Fruit neck diameter, anthocyanin index, TSS, aril juice, fruit flavor index, petiole length, fruit peel thickness and seed hardness were predominant in the first component and contributed most of the total variation. Fruit characteristics such as titratable acidity were negatively correlated (r = −0.56) with TSS (r = −0.56) and pH (r = −0.86) and also, seed hardness showed negative correlation with aril length and aril diameter. Clustering from morphological data allocated individuals into two main clusters with high variation. Two hundred and twenty-nine fragments were scored of which 174 of them were polymorphic with 76.9 % polymorphism. Genetic similarity ranged from 0.15 to 0.78 with an average of 0.42, indicating high genetic variation among studied genotypes. High molecular and morphological variability indicated that this germplasm includes rich and valuable plant materials for pomegranate breeding.
