The anatomy of the Southern Apennines is a matter of compelling debate. Both thick- and thin-skinned tectonic models are proposed due to paucity of deep seismic constraints. We present new and well-defined information on the velocity structure of the mountain range by using an innovative nonlinear tomographic technique applied to refraction– wide-angle reflection data. The velocity-interface model shows a high-velocity region, with values exceeding 7 km/s, at 8–9 km depth. Such large velocities cannot be related to sedimentary rocks, and imply the presence of shallow crystalline rocks, i.e., the basement involvement in the thrust belt. The integration of our results with other geophysical data (local earthquake tomography, Bouguer and magnetic anomalies) confirms this interpretation, which strongly supports thick-skinned tectonics and has significant implications for the seismotectonics and hydrocarbon potential of the Southern Apennines. Our inversion approach can be effective in other orogenic wedges, when seismic reflection profiling fails to uniquely resolve deep complex structures.