Oblique convergence between the North American and Caribbean plates along the eastern Greater Antilles island arc has yielded the compressive Muertos margin in the backarc region. The Muertos margin is characterized by an asymmetric thrust belt with overall opposite vergence to the subduction system in the forearc region. Offshore south of Puerto Rico, this thrust belt disappears and is replaced by a succession of NE─SW- and E─W-trending deep basins and steep ridges that characterize the western Anegada passage, resulting in a complex deformation pattern. Using new high-resolution multibeam bathymetry and a dense data set of mostly new seismic reflection profiles, we studied the along- and across-strike variations of the geomorphology and shallower structure of the southern Puerto Rico offshore margin. We have identified four morphotectonic provinces: the Puerto Rican sub-basin and Muertos trough, the Muertos margin, the insular shelf and the western Anegada passage. The Muertos margin province shows two distinct slope sub-provinces: the active Muertos thrust belt formed by N─S-compression between the island arc and the Caribbean plate’s interior ─which includes lower and upper thrust belts with distinct deformational styles and lateral continuity─ and the shelf slope covered by a thick package of layered sediments highly-incised by a dense canyon network. This network is disrupted by the Investigator fault zone consisting of a 130 km-long E─W-trending band of active extensional deformation. The Investigator fault zone shows differential surface expression caused by along-strike changes in the magnitude and distribution of the deformation, though this deformation is driven by a N─S-oriented extension, and if there is any amount of strike-slip it is insignificant. In the western Anegada passage province, the Whiting basin and Whiting and Grappler ridges are formed by large dipslip normal faults driven by a NW─SE-oriented extensional regime. The western St. Croix rise shows a complex structure as attested by the existence of NE─SW- and E─W-oriented normal faults. The NE─SW-trending NW-dipping normal faults observed at the summit of the rise predate the E─W-bounding faults that could accommodate the extensional deformation at the Present. This study provides detailed observations on the active tectonic and sedimentary processes to help future studies assessing the natural resources and the seismic and tsunamigenic hazard in the Puerto Rico region.