Genetic diversity of 74 T. urartu genotypes was studied using 11 SSR (simple sequence repeats) markers. The number of alleles ranged from 4 to 15, with an average of 8 alleles per primer. The mean values for the expected heterozygosity (He) and polymorphism information content (PIC) over all loci and populations were 0.56 and 0.52, respectively. From a geographic viewpoint the higher diversities were observed in Jordan, followed by Syria and Turkey. Diversity revealed within countries was higher than among them, even in the same regions of the relevant countries. The analysis of molecular variance revealed that most of the genetic variability was accounted for by differences within populations (90%), with less variability among them (10%). The dendrogram generated based on Nei’s dissimilarity matrix revealed three main clusters for which the grouping patterns were not clearly associated with the geographic origins, indicating the gene flow among different countries. Principal coordinate analysis (PCoA) confirmed subgrouping obtained by cluster analysis. In general, genetic distances between geographic regions were low or moderate, which was also supported by low values of pairwise Fst. Our findings can direct the sampling strategies on T. urartu in studied regions to find beneficial alleles. The heterotic groups detected by cluster and PCoA analysis in the present study can serve as effective candidates in crossing programs to broaden the genetic base in T. urartu.