<p>Jujube (<i>Ziziphus jujuba</i> Mill.) is an important fruit species traditionally cultivated in Türkiye and well adapted to diverse ecological conditions. However, no molecular-level study has so far been conducted to investigate the genetic structure of this species in the country. In the present study, 18 seed-propagated local jujube genotypes collected from Afyonkarahisar province were analyzed for the first time using Start Codon Targeted (SCoT) markers to assess genetic diversity. A total of 10&#xa0;primers generated 1,109 bands, of which 92.98% were polymorphic. The mean polymorphic information content was 0.356, effective multiplex ratio 6.16, marker index 0.0115, discriminating power 0.777, and resolving power 5.94. The highest polymorphic information content values were obtained with primers SCoT 18, 14, 32, and 21, while the highest effective multiplex ratio was recorded with SCoT 14 (11.166). The cluster analysis dendrogram revealed two main clusters among the genotypes, and STRUCTURE analysis grouped them into four genetic clusters with evidence of partial gene flow. Principal Coordinate Analysis showed that the first three components explained 53.81% of the total variance, providing a robust visualization of inter-genotypic relationships. Overall, the results demonstrated a high level of genetic diversity among the analyzed regional jujube genotypes in Türkiye and highlighted the effectiveness of SCoT markers in detecting such variability. This study represents the first molecular characterization of local jujube germplasm in Türkiye using a regional collection from Dinar, Western Türkiye. The results provide a valuable baseline for future nationwide research and will contribute to the conservation of genetic resources and the development of breeding programs.</p> Graphical abstract <p></p>