The examination of germplasm within grapevine accessions derived from wild genotypes holds significant importance within the grapevine breeding program, particularly in the improving of cultivars and rootstocks. Due to the greater genetic variation present in wild genotypes, there is an increased possibility of possessing the desired features. The objective of this study was to determine the genetic diversity and population genetic structure of 64 grapevine genotypes using inter-primer binding site (iPBS) retrotransposon markers and simple sequence repeat (SSR) markers. A total of 236 bands were generated using iPBS markers, of which 162 bands exhibited polymorphism. A comprehensive assessment was conducted on a total of 126 SSR alleles using the SSR markers, revealing that 91 of these exhibited polymorphisms. Despite the similarity in mean values between polymorphic bands generated by iPBS (6.48) and SSR markers (6.5), the iPBS markers exhibited a greater polymorphism information content (PIC: 0.39) in comparison to SSR markers (0.29). The UPGMA analysis classified the genotypes into two primary groups at a similarity index of 0.62 based on combined data. The rootstocks utilized as points of reference are consolidated inside a singular cluster (A), distinct from both the Mediterranean wild population and cultivars. The comparison of genetic variation, represented by FST values, revealed that the maximum differentiation was observed between subpopulations SP3 and SP5. The wild grapevine population grown in the Southeast Mediterranean Region of Turkey exhibited significant differentiation. Both marker systems employed in this study were highly polymorphic and useful for genetic characterization and mapping of grapevine populations.