Deep seismic profiles and subsidence history of the Gulf of Lion margin reveal an intense stretching of the distal margin and strong post-rift subsidence, despite weak extension of the onshore and shallow offshore portions of the margin. We revisit this evolution from the geological interpretation of an unpublished multi-channel seismic profile and other published geophysical data. We show that an 80 km-wide domain of thin lower continental crust, the “Gulf of Lion metamorphic core complex”, is present in the ocean-continent transition zone and exhumed mantle makes the transition with oceanic crust. The exhumed lower continental crust is bounded upward and downward by shallow north-dipping detachments. The presence of exhumed lower crust in the deep margin explains the discrepancy between the amount of extension deduced from normal faults in the upper crust and total extension. We discuss the mechanism responsible for exhumation and present two scenarios, a first one involving a simple coupling between mantle extension due to slab retreat and crustal extension, and a second one involving extraction of the lower crust and mantle from below the margin by the south-eastward flow of hot asthenosphere in the back-arc region during slab rollback. In both scenarios, the combination of Eocene crustal thickening related to the Pyrenees, the nearby volcanic arc and a shallow lithosphere-asthenosphere boundary weakened the upper mantle and lower crust enough to make them flow south-eastward. The overall hot geodynamic environment also explains the subaerial conditions during most of the rifting stage and the delayed subsidence after breakup.