The Iberian Peninsula is the only region in the world where the two existing subspecies of the European rabbit ( Oryctolagus cuniculus ) naturally occur and hybridize. In this study we explore the relative roles of historical and contemporary processes in shaping the spatial genetic structure of the rabbit across its native distribution range, and how they differently affect each subspecies and the hybrid zone. For that purpose multilocus genotypes and mitochondrial DNA data were obtained for 771 rabbits across most of the species’ distribution range in Spain. Nuclear markers defined a hierarchical genetic structure firstly comprised by two genetic groups, largely congruent with the mitochondrial lineages and subspecies distributions ( O. c. algirus and O. c. cuniculus ), which were subsequently subdivided into seven genetic groups probably shaped by environmental or ecological factors. Geographic distance alone emerged as an important factor explaining genetic differentiation across the whole range, without the need to invoke for the effect for geographical barriers. Thus, when considering the overall genetic structure, differences at a local level seem to be of greater importance. The significantly positive spatial correlation up to a distance of only 100 km supported this hypothesis. However, northern populations of O. c. cuniculus showed more spatial genetic structure and differentiation than O. c. algirus , which could be due to local geographic barriers, limited resources, soil type and/or social behaviours limiting dispersal. The hybrid zone showed similar genetic structure to the southern populations but a larger introgression from the northern lineage genome. These differences have been attributed to selection against the hybrids rather than to behavioural differences between subspecies. Ultimately, the genetic structure of the rabbit in its native distribution range is the result of an ensemble of factors, from geographical and ecological, to behavioural and molecular, that hierarchically interact in time and space.