Wild relatives of wheat are potential sources of valuable genetic materials for wheat improvement. Knowledge of the genetic diversity of wild relative species of wheat is crucial for their conservation and utilization. The objective of the current study was to investigate the genetic diversity of inter and intra species of Triticum monococcum ssp. aegilopoides (AA), Aegilops tauschii (DD) and Aegilops cylindrica (CCDD) originating from northern and western Iran. Thirty microsatellite (SSR) markers belonging to A, B, C and D genomes were used for analysis and 20 found to be polymorphic within and between species. The SSR markers generated a total number of 180 alleles with an average of 9 alleles per locus in 21 genotypes. The genetic diversity for all loci ranged from 0.74-0.90 with an average of 0.83. The highest genetic diversity was estimated for Xgwm186 and Xgwm205 which the latter could amplify in the A, D and CD genomes of T. monococcum, Ae. tauschii and Ae. cylindrica, respectively. In addition, the number of bands generated by Xgwm205 along with other four markers in Ae. cylindrica (CD) was twofold than that of Ae. tauschii (D). Polymorphic information content ranged from 0.7-0.89 with an average of 0.82. The dendrogram obtained from the neighbor-joining method divided the genotypes of the three species into three distinctive groups. It can be concluded that SSR markers can be useful not only in differentiating wild species of wheat possessing A, D and C genomes, but also in assessing the genetic variation of genotypes within these species.