In the South Gabon Basin, deep multi-channel seismic reflection and gravity modeling analysis have shed light on key features of the structure of the margin. The thinned continental crust beneath the Gabon Margin appears to be composed of two distinct layers, separated by a clear, strong and more or less continuous reflector running in the 7–10 s TWT window. The lower crust is characterized by a higher density, intermediate between the lower values of the upper crust and the denser values of the mantle. The lower crust is irregularly shaped and presents lateral thickness variations along the direction of thinning and along the coast. In the offshore thinned continental domain, the lower and upper crust form a 20–25 km thick body. Crustal thicknesses point to a relatively sharp and narrow transition, along a few tens of kilometers, between the unthinned and the thinned continental crust. The high density layer identified offshore Gabon presents similar characteristics in density, geometry and spatial distribution, as the underplated magmatic bodies observed along volcanic margins, e.g. along the South Atlantic Namibia Margin or the North Atlantic Vøring Margin. Although this lower crustal body could possibly represent ultra mafic serpentinized rocks or high grade metamorphic crustal rocks, we suggest that it could be composed of mafic rocks. Magmas resulting from partial melting during rifting may underplate the crust and/or be intruded in the lower crust through a system of dykes and sills. In this view, the present-day crustal thicknesses along rifted margins, characterized by magmatic underplating and/or intrusion, are not representative of the thinning that the crust experienced during rifting. Results of this study point to relatively shallow sedimentary basins along the South Gabon Margin. The deepest offshore depocenters located under the westernmost side of the continental platform appear to be associated with the deepest syn-rift basins These basins seem to extend along 20 to 40 km in the ~ NE–SW direction with a present-day average thickness of 7.3 km. Offshore Gabon, whereas the crustal thinning appears significant, the syn-rift deposit are not thick. We suggest that the area was anomalously uplifted during the rifting phase, due to an elevated thermal lithospheric gradient. The conclusions derived from our seismic and gravity analysis are consistent with the implications such a thermal anomaly would have on the tectonic evolution of a rifted margin with 1) an underplated high density lower crustal layer, 2) shallow depth syn-rift basins associated with a relatively thin crust and subsequently 3) elevated recorded subsidence rates in the initial post-rift stages. Research Highlights ► The Gabon Margin appears characterized by an underplated high density lower crustal layer. ► Shallow depth syn-rift basins are associated with a relatively thin crust. ► Seismic and gravity analysis points to an anomalous uplift of the Gabon Margin during the rifting phase. ► Crustal structure, syn-rift infill and post-rift subsidence are consistent an uplift of the Gabon Margin during the rifting phase. ► The uplift of the Gabon Margin is possibly due to an elevated thermal lithospheric gradient.