Investigating when, where, and how domestication took place is crucial for understanding cultural and evolutionary transitions in the history of crop species. The olive (Olea europaea subsp. europaea) is often considered the most iconic tree of the Mediterranean Basin, probably domesticated in the Levant 6000 years ago. Recent genetic study has suggested that an area near the border between Turkey and Syria is the primary center of domestication. To examine this assumption on a local scale, we sampled wild olive populations from this area in the south Taurus Mountains and analyzed them in comparison with Turkish cultivars using nuclear and chloroplast DNA markers. Using principal component analysis, genetic distance clustering and Bayesian structure, we classified Turkish olive into wild and domesticated gene pools. Some cultivars were completely or partially assigned to the wild pool, supporting the assumption of local domestication from wild Turkish populations. Concurrently with this genetic investigation, excavation of an early Neolithic settlement in the Taurus region, Yumuktepe, provided some information on 9000 years of the agricultural environment through the discovery of the earliest known carbonized olive remains, found in the dwellings, showing that harvesting of wild olive is an old tradition in Anatolia. Our findings are important to extend the gene pool for breeding to wild olive populations with interesting adaptive traits.