The deep crustal features at the transition from the Pyrenean range to the NW Mediterranean basin have been investigated by onshore/offshore recording of LIgurian SArdinian (LISA) seismic profiles. The predominance in this area of the Neogene extensional tectonics over the Paleogene compressional one is revealed from the present‐day deep structure sampled by the new wide‐angle data. The existence of a crustal root beneath the Pyrenean Axial Zone and the outstanding differences in Moho depths between the Iberian and European domains, well established from previous seismic studies on central and western Pyrenees, are not observed anymore at the easternmost part of the range. This area is marked by a continued crustal thinning seawards (the Moho rises about 10 km along distances of 60 km) that affects already the mainland. Further evidences on lateral variations and topography of the crust‐mantle boundary are indicative of the extent of the different tectonic episodes.