SUMMARY New seismic reflection profiles of the Italian deep crust project CROP provide new insights on the structure of the Ionian sea. In spite of the Apennines and Hellenides Neogene subduction zones, two conjugate passive continental margins are preserved at the margins of the Ionian sea, along the Malta escarpment to the southwest and the Apulian escarpment to the northeast. The Ionian sea is likely to be a remnant of the Mesozoic Tethys Ocean, confined by these two conjugate passive continental margins. The transition from continental to oceanic crust appears sharper to the northeast than to the southwest. The basin between southeast Sicily and southwest Puglia was about 330 km wide and suggests a low spreading rate. The inferred oceanic ridge should have been flattened by thermal cooling and buried by later sediments. Based on stratigraphic and structural constraints to the north in the Apennines belt, the ocean continued to the northwest. This palaeogeography is supported by the seismicity of the Apennines slab underneath the southern Tyrrhenian sea, which implies downgoing oceanic lithosphere. The adjacent absence or paucity of deep seismicity does not imply absence of subduction, but rather it can be interpreted as due to the more ductile behaviour of the subducted continental lithosphere. Surprisingly, we note that where the oceanic inherited basin is subducting underneath the Apennines, in the hangingwall of the subduction hinge there are outcropping slices of continental crystalline basement previously deformed by the Alpine orogen.