The relationships among 55 wheat accessions (47 accessions collected from Iran and eight accessions provided by the Institute of Plant Biology of the University of Zurich, Switzerland) belonging to eight species carrying A genome (Triticum monococcum L., T. boeoticum Boiss., T. urartu Tumanian ex Gandilyan, T. durum Desf., T. turgidum L., T. dicoccum Schrank ex Schübler, T. dicoccoides (Körn. ex Asch. & Graebner) Schweinf. and T. aestivum L.) were evaluated using 31 A genome specific microsatellite markers. A high level of polymorphism was observed among the accessions studied (PIC = 0.77). The highest gene diversity was revealed among T. durum genotypes, while the lowest genetic variation was found in T. dicoccoides accessions. The analysis of molecular variance (AMOVA) showed a significant genetic variance (75.56%) among these accessions, representing a high intra-specific genetic diversity within Triticum taxa in Iran. However, such a variance was not observed among their ploidy levels. Based on the genetic similarity analysis, the accessions collected from Iran were divided into two main groups: diploids and polyploids. The genetic similarity among the diploid and polyploid species was 0.85 and 0.89 respectively. There were no significant differences in A genome diversity from different geographic regions. Based on the genetic diversity analyses, we consider there is value in a greater sampling of each species in Iran to discover useful genes for breeding purposes.