Understanding domestication in perennial crops is crucial for unraveling the evolutionary trajectories that shaped their genetic diversity and for guiding conservation and breeding. The domestication of Mediterranean fruit trees is less studied than that of annual crops. The common fig (Ficus carica L.) is thought to have been domesticated in the Levant before dispersal across the Mediterranean; however, prehuman fossils in Europe suggest an ancient wild presence, challenging the assumption of a single eastern origin. We genotyped 949 cultivated and spontaneous fig accessions using microsatellite markers from 14 Mediterranean and Near Eastern countries, as well as F. carica subsp. rupestris and Ficus colchica. Principal component analysis showed that F. carica sensu stricto forms a cohesive genetic group distinct from its relatives, which should be considered separate species. Bayesian clustering revealed three major gene pools within F. carica sensu stricto—Moroccan–Algerian, Northern Mediterranean, and Levantine—each containing both cultivated and spontaneous individuals. The Levantine group was the most differentiated, while the other two were more closely related, reflecting a longitudinal Mediterranean structure. Cultivated and spontaneous figs were genetically indistinguishable within regions, supporting a diffuse, regionally independent domestication model rather than a single Levantine origin. These results highlight spontaneous populations and local landraces as critical reservoirs of genetic variation in Morocco, Algeria, and the Levant. Our study provides a foundation for genomic research to identify the basis of key traits and emphasizes that breeding and conservation strategies should rely on regional biodiversity to enhance fig resilience and productivity under global change.

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