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Among the wild relatives of wheat, Triticum urartu Tumanian ex Gandilyan is of interest to wheat breeders. Numerous works have focussed on its utilization for enrichment of the genetic variation of cultivated genotypes. In the present study, the genetic diversity and population structure in 85 accessions of T. urartu were investigated using start codon targeted (SCoT) polymorphism and CAAT-box derived polymorphism (CBDP) markers. Nineteen SCoT primers and fifteen CBDP primers amplified 185 and 141 polymorphic fragments with an average of 9.74 and 9.40 fragments per primer, respectively. The polymorphic information content (PIC) for the SCoT and CBDP primers ranged from 0.41 to 0.50 and 0.40 to 0.49, with the resolving power (Rp) ranging from 21.61 to 3.97 and 13.08 to 28.02, respectively. Neighbour-joining (NJ) based clustering grouped 72 accessions into two main clusters based on the two sets of markers and the combined data. Genetic relationships inferred from STRUCTURE analysis was matched with cluster analysis and principal coordinate analysis (PCoA), indicating that the accessions were grouped into two major clades and the grouping patterns were not correlated with the geographic origins. The results from this study revealed that Iranian T. urartu, especially Kerend-e-Gharb and Sisakht-Pataveh populations, can be interesting for wheat improvement. Hence, conservation of this region is recommended. [ABSTRACT FROM AUTHOR]