ABSTRACT. The study aimed to analyze 90 wild pomegranate genotypes collected from six geographical regions of Azerbaijan. A total of 110 PCR fragments were amplified, 86 of which were found to be polymorphic. The number of amplified fragments per primer ranged from 5 to 10, with an average of 7.8. Polymorphic DNA fragments varied from 3 to 9, with a mean of 6.1. Polymorphism percentage ranged from 57% to 100% depending on the primer, averaging 78% overall. The genetic diversity index (GDI) had a mean value of 0.77, with the highest values observed for the IS15 (0.92), UBC811 (0.90), and HB14 (0.90) primers. Cluster analysis grouped accessions into five main clusters, with the genetic similarity index ranging from 0.03 to 1.00. The outcomes of the cluster analysis unveiled the grouping of most accessions based on their collection sites. Results indicate significant diversity in wild pomegranate germplasm in Azerbaijan, suggesting adaptability to various environmental conditions. Further molecular analysis can elucidate the phylogenetic relationships among genotypes, aiding in the understanding of domestication processes in the future.