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Abstract: In the present research, we used microsatellite markers to study the genetic diversity and phylogenetic analysis among 75 pomegranate genotypes from Iran, Japan, Turkmenistan, Russia, Italy and USA. Ten out of 25 primer pairs showed 12 polymorphic loci and revealed 38 alleles with an average of 3.1667 alleles per locus and the mean of polymorphic information content (PIC) was calculated as 0.358. Comparing the group of genotypes from different countries revealed that the Iranian genotypes have the highest genetic diversity. The analysis of molecular variance (AMOVA) showed that the high level of genetic diversity occurred within groups and low level of that obtained among them. According to the results, most of the Russian accessions clustered with the Iranian genotypes and some of the American genotypes were grouped with Turkmenistan accessions. Also unknown genotypes showed the close relationships to Turkmenistan and Iranian ones. The results could show the existence of the common ancestors among the genotypes and probably confirms the hypothesis that pomegranate spread from central Asia, especially parts of Iran and neighboring areas such as Turkmenistan to other regions of the world. [Copyright &y& Elsevier]