<p>Wild cherry plum (<i>Prunus cerasifera</i> Ehrh.) is a fruit species of high agronomic, ecological, and economic importance. In this study, the genetic diversity and population structure of 100 wild cherry plum genotypes collected from different geographical regions of Azerbaijan were evaluated using Inter Simple Sequence Repeat (ISSR) molecular markers. Using the 20 ISSR primers employed in the study, a total of 157 loci were amplified, of which 128 (81.9%) were polymorphic, indicating a high level of genetic variation among the genotypes. The number of bands detected per primer ranged from 5 to 11, with an average of 7.9. The polymorphism information content (PIC) values ranged from 0.15 to 0.49, with an average PIC of 0.39. An average genetic diversity index (GDI) value of 0.91 confirmed that the population is genetically rich and highly heterogeneous. Cluster analysis revealed that the genotypes were grouped into five major clusters, showing a minimal association with their geographical origin. Principal coordinate analysis (PCoA) also indicated very low geographical structuring among the genotypes. Analysis of molecular variance (AMOVA) revealed that 96% of the total genetic variation was distributed within groups, while only 4% was attributed to variation among groups. The fixation index (Fst = 0.044) indicated a low level of genetic differentiation among populations, while the estimated gene flow (Nm = 5.47) suggested the presence of substantial genetic exchange among them. The Mantel test revealed an exceptionally high correlation between the matrices (r = 0.999, p &lt; 0.001), confirming that the genetic divergence among the samples accurately reflects their spatial distribution. The results obtained confirm that ISSR markers are an effective molecular tool for assessing the genetic diversity of wild cherry plum genotypes. Furthermore, they highlight the significant value of Azerbaijan’s <i>Prunus cerasifera</i> Ehrh. populations for breeding programs and the conservation of genetic resources.</p>