Detailed analyses of seismic profiles and boreholes in the Valencia Basin (VB) reveal a differentiated basin, the Minorca Basin (MB), lying between the old Mesozoic Valencia Basin sensu strico (VBss) and the young Oligocene Liguro-Provençal Basin (LPB). The relationship between these basins is shown through the correlation of four Miocene-to-present-day megasequences. The Central and North Balearic Fracture Zones (CFZ and NBFZ) that border the MB represent two morphological and geodynamical thresholds that created an accommodation in steps between the three domains. Little to no horizontal Neogene movements are found for the Ibiza and Majorca Islands. In contrast, the counterclockwise movement of the Corso-Sardinian blocks induced a counterclockwise movement of the Minorca block towards the SE along the CFZ and NBFZ, during the exhumation of lower continental crust in the LPB. This new understanding implies pure Neogene vertical subsidence in the VBss and places the AlKaPeCa northeastward of the present-day Alboran Area.