Resolving tectono-stratigraphic relationships, critical for using syn-tectonic sedimentation to calibrate time and length scales of processes in the Apennine-Maghrebian orogenic system, is difficult using outcrop data alone. Here two commercially-acquired seismic reflection profiles are used to establish the structure and stratigraphic relationships between the frontal part of the orogenic belt, the foredeep and foreland regions in the offshore continuation of the Apennine system in the northern Ionian sea. Seismic stratigraphic reasoning is used to define an inter-regional intra-Messinian unconformity surface. In the Apulian foreland this is cut by a widespread array of normal faults that are sealed by Plio-Quaternary sediments. The modern foredeep is in part controlled by these faults. On the Apulian shelf the deposystems are broad. However, the modern foredeep and basins developed on the orogenic wedge are only a few km across. Given the proximity of this study area, the tectono-stratigraphic relationships imaged on these seismic lines are likely to provide good analogues for Neogene basins and depositional systems for much of the Apennines onshore. Syntectonic basins are narrow, long-range stratigraphic continuity is likely to be the exception rather than the rule. This challenges some of the assumptions behind existing tectonic models for the Apennines and similar orogens.