Marine protected areas (MPAs) require ecologically meaningful designs capable of taking into account the particularities of the species under consideration, the dynamic nature of the marine environment, and the multiplicity of anthropogenic impacts. MPAs have been most often designated to protect benthic habitats and their biota. Increasingly, there is a need to account for highly mobile pelagic taxa, such as marine birds, mammals and turtles, and their oceanic habitats. For breeding seabirds foraging from a central place, particular attention should be paid to distant foraging grounds and movement corridors, which can often extend to hundreds of kilometers from breeding colonies. We assessed the habitat use by the most threatened Mediterranean seabird, the Balearic Shearwater, Puffinus mauretanicus, using vessel-based surveys during the chick-rearing period (May-June). We used a hierarchical modeling approach to identify those environmental variables that most accurately reflected the oceanographic habitat of this species by (1) delineating its foraging range using presence/ absence data and (2) identifying important foraging grounds where it concentrates in dense aggregations. The foraging range comprised the frontal systems along the eastern Iberian continental shelf waters (depth <200 m) and areas close to the breeding colonies in the Balearic Islands. Shearwaters aggregated in productive shelf areas with elevated chlorophyll a concentrations. Following the model of a core-buffer MPA, we envisioned those areas of dense aggregation (i.e., the area of influence of the Ebro River discharge and Cape La Nao regions) as the core regions deserving elevated protection and more stringent management. More diffuse protective measures would be applied within the larger buffer region, delineated by the foraging range of the species. Marine zoning measures can greatly benefit the conservation of the Balearic Shearwater and other far-ranging seabirds by extending protective measures beyond their breeding colonies during both the breeding and non-breeding seasons.