This study investigates the phenotypic characteristics, genetic diversity, and population structure of four wild cherry species collected from various regions of Kazakhstan and Uzbekistan: Prunus fruticosa Pall., Ptunus erythrocarpa (Nevski) Gilli, Prunus griffithii var. tianshanica (Pojark.) Ingram, and Prunus verrucosa (Franch.). A total of 163 accessions were characterized morphologically using standardized descriptors for plant, leaf, and fruit traits. Genetic diversity was assessed using 13 simple sequence repeat (SSR) markers. STRUCTURE analysis revealed that 87.7% of the accessions were assigned to pure species. However, hybrid accessions were identified in P. griffithii var. tianshanica (34.4%), P. erythrocarpa (18.5%), and P. verrucosa (8.0%). Identical genotypes were found across all species, with P. fruticosa showing the highest proportion (54.8%), likely due to clonal propagation via root suckers. Among the four species, P. verrucosa exhibited the highest genetic diversity, while P. fruticosa had the lowest. Analysis of molecular variance (AMOVA) showed that genetic variation within the species (81%) was substantially greater than variation among the species (19%). These findings enhance our understanding of the genetic relationships among wild cherry species in Central Asia and provide valuable data for conservation planning and breeding programs aimed at improving drought and frost tolerance in Prunus species.