The wild grapevine (Vitis vinifera subsp. sylvestris Gmel. Hegi) is a dioecious subspecies considered as ancestor of the cultivated grapevine (Vitis vinifera L.). Due to high human pressure to natural plant resources in the last hundred years accompanied with pest, diseases and global climate change, the wild grapevine is highly threatened. The diversity of wild grapevine is poorly represented in gene banks while their habitats constantly declining. The wild grapevine in Slovenia, Croatia and Bosnia and Herzegovina are poorly known. Therefore, current study inventoried remaining populations of wild grapevine in this territory and evaluated their morphological and genetic traits. The inventory started in 2015 confirming several historical populations in eastern Adriatic regions but also finding some new ones not recorded up to now. During prospecting, wild grapevines were found at eight geographically distant locations in this territory. Each observed individual was considered to meet truly morphological criteria (dioecism and leaf morphology) for sylvestris. Ninety-eight sylvestris individuals belonging to 8 populations have been genotyped at 20 nuclear simple sequence repeats (SSR) loci to detect genetic diversity. Distance- and model-based cluster analysis differentiated among samples highlighting at least three different groups. The results showed the existence of considerable level of genetic diversity of wild grapevine but also hidden alleles that could be of interest for breeding programs. The study provides necessary information for conservation management and further characterization of wild grapevine.