In this study, morphological characteristics as well as ten of Simple Sequence Repeat (SSRs) loci were used to analyze the genetic diversity and relationships among 12 natural populations of Persian walnut (Juglans regia L.) in northern and western regions of Iran. The results showed that there was a high level of genetic diversity among the walnuts, both in terms of their SSRs loci as well as morphological traits. The nut weight ranged from 11.5 to 17.2 g, kernel weight from 3.2 to 6.3 g, and kernel percentage from 28 to 46.7%. In SSRs analysis, the number of alleles per locus ranged from 6 to 11, with a total of 83 alleles and average of 8.3 alleles and 4.9 effective alleles per locus. The expected heterozygosity (He) varied between 0.70 and 0.87, with an average of 0.79 per locus. The proportion of genetic differences among the walnut populations accounted for 19% of the total variation. The overall gene flow among populations equaled 1.10. The 12 walnut populations were separated into four main groups via the unweighted pair group method (UWPGM) with arithmetic mean cluster analyses based on Nei’s unbiased genetic distances.
