This study was conducted to analyze genetic diversity in 15 natural populations of Iranian Agropyron pectiniforme using morphological traits and RAPDs (Random Amplification of Polymorphic DNA) molecular markers. Five primers out of the 10 were highly polymorphic and produced 128 polymorphic bands ranging in length of 500 to 2200 bp. According to AMOVA (Analysis of Molecular Variance) results, there was higher genetic variation between populations (53%) than within (47%) them. Cluster analysis based on RAPD data categorized the populations into five clusters. PCoA (Principal Coordinates Analysis) results showed the first four coordinates accounted for 95% of the total variation. The scatter of genotypes based on the first two components was agreement with cluster analysis results. There was non-significant mantel correlation coefficient between molecular and geographical data indicating classification of A. pectiniforme based on RAPD marker was not in accord with geographical distribution. With regard to morphological traits, characters including plant height and the number of stems per plants are suitable parameters for selection of potential parents in the breeding programs. The non-significant mantel correlation coefficient between molecular and morphological marker was observed, then suggested that the two marker systems give different estimates of genetic relations among populations. Finally, our findings demonstrate the feasibility of the RAPD technique for quantifying genetic distances among A. pectiniforme populations. It was concluded that, there is sufficient genetic variation between Iranian populations of Agropyron pectiniforme which these genotypes can be useful for germplasm improvement and cultivar development. Manuscript profile