The Fertile Crescent of Southwest Asia holds high genetic diversity of crop species of the grass tribe Triticeae, which provide staple food for the majority human population. Genetic diversity and their relationships were studied among 51 accessions from Aegilops and Triticum species from Iraqi Kurdistan.Eighteen SCoT markers were used to generate a total of 139 alleles. The discriminating power of the markers was assessed with polymorphism information content (PIC) and marker index (MI), that valued at 0.56 and 3.7, respectively. These results indicate the informativeness of the markers used for studying genetic diversity among the Aegilops and Triticum species. A high level of diversity was identified among the accession, to separate three distinct groups based on the SCoT data. All the accessions from different species with an 'A' genome were clustered together in a group, including Aegilops tauschii (possessing D genome). While the other Aegilops (U genome) were clustered in the other two groups. Analysis of molecular variance (AMOVA) partitioned 62% of variability among populations, while 38% of variation was considered between accessions within populations. Principal coordinate analysis (PCoA) for SCoT data showed that the first two components clarified 54.73% of the total variation, indicating consistent patterns of genetic relationships between the accessions. Genetic relationships inferred from UPGMA dendrogram analysis were matched with the PCoA, indicating that the grouping patterns of the accessions were in agreement with their botanical classifications. These results obtained could allow for future insight into wheat breeding programs.