<p>Deciphering genetic diversity and population structure is crucial for development of sustainable crop breeding programs. Wheat, as one of the most important staple crops, plays a pivotal role in providing essential energy and ensuring food security. The development of new cultivars or the expansion of the genetic basis for improved cultivars depends on the discovery of novel allelic variations within germplasm resources. In this study, a molecular assessment was conducted on 325 selected accessions representing 13 species of <i>Triticum</i> and <i>Aegilops</i> using CAAT-box derived polymorphism (CBDP) markers. Fifteen primers generated 199 fragments across the accessions studied, of which 196 were polymorphic. Key genetic parameters, including the number of amplified fragments and polymorphic fragments (NAF and NPF), polymorphic information content (PIC), resolving power (Rp), and marker index (MI) were estimated at 13.27, 13.07, 0.38, 16.06, and 5.01, respectively. Analysis of molecular variance (AMOVA) indicated that genetic variations within genera and species exceeded variation among them. At the species level, <i>T. boeoticum</i>, <i>T. urartu</i>, and <i>Ae. triuncialis</i> exhibited the highest values for genetic variation compared to other species. Multivariate analyses, including cluster analysis and principal coordinate analysis (PCoA), demonstrated that individual groupings were consistent with their genetic backgrounds. These findings were corroborated by population structure analysis, which revealed that two sub-species of <i>Ae. tauschii</i> formed distinct sub-groups. The results suggest that CBDP markers represent a valuable genotyping tool with substantial potential for phylogenetic research. Furthermore, they may prove particularly effective for genetic investigations, such as mapping quantitative trait loci (QTL)&#xa0;and association analyses, particularly when combined with co-dominant marker techniques.</p>