High-velocity lower crust (HVLC) and seawarddipping reflector (SDR) sequences are typical features of volcanic rifted margins. However, the nature and origin of HVLC is under discussion. Here we provide a comprehensive analysis of deep crustal structures in the southern segment of the South Atlantic and an assessment of HVLC along the margins. Two new seismic refraction lines off South America fill a gap in the data coverage and together with five existing velocity models allow for a detailed investigation of the lower crustal properties on both margins. An important finding is the major asymmetry in volumes of HVLC on the conjugate margins. The seismic refraction lines across the South African margin reveal cross-sectional areas of HVLC 4 times larger than at the South American margin, a finding that is opposite to the asymmetric distribution of the flood basalts in the Paraná–Etendeka Large Igneous Province. Also, the position of the HVLC with respect to the SDR sequences varies consistently along both margins. Close to the Falkland–Agulhas Fracture Zone in the south, a small body of HVLC is not accompanied by SDRs. In the central portion of both margins, the HVLC is below the inner SDR wedges while in the northern area, closer to the Rio Grande Rise-Walvis Ridge, large volumes of HVLC extend far seaward of the inner SDRs. This challenges the concept of a simple extrusive/intrusive relationship between SDR sequences and HVLC, and it provides evidence for formation of the HVLC at different times during the rifting and breakup process. We suggest that the drastically different HVLC volumes are caused by asymmetric rifting in a simple-shear-dominated extension.