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Societal Impact Statement Crop wild relatives (CWR) are valuable sources of genetic diversity for plant breeding. However, the identification of wild untapped genetic resources (i.e., unexploited in crops) is not always straightforward. We propose a methodology to guide the identification and conservation of these resources that integrates both genetic and ecological data. This approach enabled us to identify approximately 50 exceptional wild olive tree populations throughout the species' range that should be the focus of immediate conservation. Furthermore, our methodology is adaptable and can be applied to other plants and animals facing the same problem, making it widely useful for biological conservation. Summary Crop wild relatives (CWR) tend to harbor wider ecological, genetic, and phenotypic diversity than their cultivated counterparts. The recognition of their potential has led to the development of specific conservation plans. Nonetheless, the distinctiveness and conservation urgency of CWR pools vary considerably, making case‐specific strategies necessary. Here, we use wild olive ( Olea europaea L.) to develop a framework for the identification, management, and conservation of CWR that exhibit sympatry and frequent introgression with cultivated forms. This strategy employs genetic and ecological data to prioritize untapped genetic resources. We compiled the available phylogeographic data from 118 wild olive populations spanning all known cpDNA lineages and five O. europaea subspecies distributed across the Mediterranean basin, Macaronesia and Saharan Africa, and classified all populations according to their genetic diversity and dissimilarity to the cultivated gene pool. Furthermore, we used a Species Distribution Model (SDM) and an environmental Principal Component Analysis (PCA‐env) to identify oleaster ( O. e . subsp. europaea var. sylvestris ) accessions under extreme ecological conditions or highly vulnerable to climate change. Our analyses identified populations with unique genetic and/or ecological features, as well as areas where wild olive has high agronomic and ecological value but remains unprotected and/or its persistence is threatened by climate change. Based on these results, we highlight 53 wild olive populations in Saharan Africa, Macaronesia, and the Mediterranean basin as priority conservation targets. More broadly, the methodology outlined here provides a transferable framework for safeguarding the diversity of other CWR with available ecological and genetic data.