In Azerbaijan, along the banks of the Kura River and in the Karabakh region, both table and technical grape varieties are cultivated, alongside wild grape varieties. Since ancient times, unripe and ripe fruits of wild Caucasian grapes have been used in medicine, agriculture, and the preparation of special sauces. Studying the genetic resources and biodiversity between wild and cultivated grapes (Vitis spp.) is crucial for understanding evolutionary processes, developing conservation strategies, and improving breeding programs aimed at grapevine enhancement. This study investigates the genetic diversity and evolutionary relationships between wild grape genotypes (V. vinifera subsp. sylvestris) and ancient, valuable cultivated grape varieties (V. vinifera subsp. vinifera) found around the Kura River in Azerbaijan. It was aimed to detect genetic diversity among grape samples of Azerbaijani origin using Random Amplified Polymorphic DNA (RAPD)-based genotyping analysis. A total of 21 genotypes, including six wild and fifteen cultivated genotypes, were evaluated. Percentage genetic similarities, polymorphism information content (PIC), and resolving power (RP) values were calculated. The minimum similarity between Shirvan-Shahı samples and wild grape samples is 50 percent. The highest genetic similarity was observed between VS6 and VVSH varieties with a similarity index of 0.954.

Mean RP and PIC values were as 3.34 and 0.43, respectively. The results revealed that the average genetic similarity among V. vinifera samples was higher than the average similarity index among wild genotypes. Additionally, a high genetic proximity index was observed between some cultivated samples and wild varieties. This research reveals significant genetic differentiation and hybridization events, highlighting unique alleles in wild grapevines that contribute to stress resistance and environmental adaptability. It also provides insights into many historical domestication processes, emphasizing the importance of preserving genetic diversity and proposing strategies to enhance grapevine cultivars’ resilience against climate change, pests, and diseases. These findings suggest the need for further molecular marker studies to clarify the evolutionary relationships and origins of these wild grapevines.