The Red Sea is an important example of a rifted continental shield proceeding to seafloor spreading. However, whether the crust in the central Red Sea is continental or oceanic has been controversial. Contributing to this debate, we assess the basement geometry using seismic reflection and potential field data. We find that the basement topography from seismically derived structure corrected for evaporite and other sediment loading has an axial high with a width of 70–100 km and a height of 0.8–1.6 km. Basement axial highs are commonly found at mid-ocean ridges affected by hotspots, where enhanced mantle melting results in thickened crust. We therefore interpret this axial high as oceanic-like, potentially produced by recently enhanced melting associated with the broader Afar mantle anomaly. We also find the Bouguer gravity anomalies are strongly correlated with basement reflection depths. The apparent density contrast necessary to explain the Bouguer anomaly varies from 220 kg m−3 to 580 kg m−3 with no trend with latitude. These values are too small to be caused primarily by the density contrast between evaporites and mantle across a crust of uniform thickness and density structure, further supporting a thickened crustal origin for the axial high. Complicating interpretation, only a normal to modestly thickened axial crust is predicted from fractionation-corrected sodium contents (Na8.0), and the basement reflection is rugged, more typical of ultra-slow spreading ridges that are not close to hotspots. We try to reconcile these observations with recent results from seismic tomography, which show modest mantle S-wave velocity anomalies under this part of the Red Sea.