Iran is in possession of the richest gene pool of pomegranate, with an amazing diversity and number of genotypes, in the world. In this study RAPD markers were mployed to determine the level of diversity, and phylogenetic relationships among 24 Iranian pomegranate genotypes. Genomic DNA extracted from leaves, and its quantity as well as quality were determined by use of spectrophotometry and agarose gel electrophoresis to be used for PCR after being adjusted for the concentrations. In total 113 primers were used for PCR reactions on the template DNAs among which 27 showed reasonable amplification and polymorphism. Bands with a acceptable resolution and high repeatability were selected for calculations. These 27 primers produced 257 bands, among them, 158 were polymorphic. Cluster analysis of the genotypes was performed based on the presence (1) or absence (0) of the bands, using Jaccard’s similarity coefficient and UPGMA method. The highest and lowest observed genetic similarity between genotypes was 0.88 and 0.30 respectively. At a distance of 0.64 similarities on the dendrogram, the genotypes were divided into 8 sub-clusters. A Cophenetic coefficient of r=0.92 between similarity matrices and the dendrogram is an indication of the dendrogram properly fitting the similarity data. The examined genotypes were to relatively high diversity, implying the richness of pomegranate genetic resources in Iran. Furthermore, this study reflected the possibility of similar names having been given to different genotypes or the mistakes and mixes in either collection establishments or during translocation of genotypes. Besides, RAPD markers were shown to be a useful technique for studying the genetic diversity in pomegranate
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