Background <p>Olive pedigree has been scarcely explored beyond domestication and diversification studies, even though it can be valuable for breeding programs and germplasm management. This study presents a new and comprehensive exploration of olive parentage relationships by combining a large dataset of 840 cultivars with a cost-effective and highly informative panel of 96 EST-SNP markers routinely applied at the World Olive Germplasm Bank of Córdoba. Parentage assignments were performed combining two approaches, SambaR and CERVUS, and using 13 seedlings of known crosses as validation controls.</p> Results <p>This strategy revealed 1,218 parent-offspring duos and 280 robust parent-parent-offspring trios, involving more than 85% of the individuals analysed. Four founder cultivars, ‘Gordal Sevillana’, ‘Lechín de Granada’, ‘Toffehi Tataouine’, and ‘Safrawi’, emerged as central nodes in the pedigree network, highlighting their crucial role in the diversification of olive cultivars across the Mediterranean Basin. ‘Gordal Sevillana’, in combination with ‘Lechín de Granada’ and ‘Toffehi Tataouine’, contributed substantially to the origin of Western and, to a lesser extent, Central Mediterranean cultivars, while ‘Safrawi’ acted as a key connector across the entire basin.</p> Conclusions <p>This study provides the first olive parentage atlas, providing new insights into the diversification processes, but also a practical tool for the management of genetic resources. In particular, these results demonstrate that a small but informative SNP set can generate reliable pedigree information to identify compatible parents, resolve uncertain genealogies of cultivars of agronomic interest, reconstruct unknown pedigrees in open-pollination, and guide the selection of balanced parental sets for developing new cultivars.</p>