AbstractIn continental settings, seismic failure is generally restricted to crustal depth. Crustal structure is therefore an important proxy to evaluate seismic hazard of continental fault systems. Here we present a seismic velocity model across the Gibraltar Arc System, from the Eurasian Betics Range (South Iberian margin), across offshore East Alboran and Pytheas (African margin) basins, and ending onshore in North Morocco. Our results reveal the nature and configuration of the crust supporting the coexistence of three different crustal domains: the continental crust of the Betics, the continental crust of the Pytheas Basin (south Alboran Basin) and onshore Morocco, and a distinct domain formed of magmatic arc crust under the East Alboran Basin. The magmatic arc under the East Alboran Basin is characterized by a velocity structure containing a relatively high‐velocity lower crust (~7 km/s) bounded at the top and base by reflections. The lateral extension of this crust is mapped integrating a second perpendicular wide‐angle seismic profile along the Eastern Alboran basin, together with basement samples, multibeam bathymetry, and a grid of deep‐penetrating multichannel seismic profiles. The transition between crustal domains is currently unrelated to extensional and magmatic processes that formed the basin. The abrupt transition zones between the different crustal domains support that they are bounded by crustal‐scale active fault systems that reactivate inherited structures. Seismicity in the area is constrained to upper‐middle crust depths, and most earthquakes nucleate outside of the magmatic arc domain.