Two geophysical onshore-offshore lines on the southern margin of Africa form the Agulhas-Karoo Geophysical Transect (AKGT) and cross prominent geological features such as the Karoo Basin, Cape Fold Belt (CFB) and the Beattie Magnetic Anomaly (BMA). Geophysical data acquired along this AKGTransect between 2004 and 2007 within the Inkaba yeAfrica (lyA) framework, provide the platform for constructing a deep crustal section (IyA-200501) for the centre 100 km of the western AKGT-transect in order to resolve these features at depth. We present a detailed deep crustal model constructed from the joint interpretation of: i. archive data comprising surface geology, aeromagnetic data, nearby deep boreholes, teleseismic receiver functions and regional seismic reflection profiles, and ii. line coincident newly acquired high-resolution geophysical data consisting of near vertical seismic reflection data, shallow P- and S-wave velocity data, wide-angle refraction data, high resolution magnetotelluric data and impedance spectroscopy measurements on borehole samples. Our model differentiates four components in the up to 45 km thick crust: 1. a ~2 to 5 km thick folded Karoo Supergroup, disrupted by low-angle thrust faults rooted in a zone of local décollements in the lower Ecca Group and resting paraconformably on 2. a continuous undeformed sub-horizontal ~1.5 to 10 km thick wedge of the Cape Supergroup (CSG). This CSG wedge stretches from the Escarpment in the north to the tectonic front of the CFB in the south, and rests on an unconformity that dips about three degrees to the south. The angular unconformity is interpreted as an erosional peneplain that separates the CSG wedge from component 3. the ~13 to 21 km mid-crust basement below. The mid-crust contains a distinct north-dipping seismic fabric, here interpreted as ~1.4 to 1.0 Ga Mesoproterozoic Namaqua-Natal Metamorphic Belt (NNMB) crust. A south-dipping mid-crustal detachment, interpreted as a ductile thrust zone, separates the mid-crust from component 4. a highly reflective ~10 to 24 km thick lower crust. The latter is interpreted as an older Palaeoproterozoic section of the NNMB (or even Archean cratonic basement), and bounded by a ~2 to 5 km thick, highly reflective bottom layer below that lies sub- parallel to a clear Moho. This bottom layer is interpreted as a mafic underplate, metasomatic reaction zone, or lower-crust to mantle transition zone. Collectively the seismic reflection and wide-angle refraction data support an interpretation that the NNMB mid-crustal layer contains the BMA source, possibly connected to two zones of strong reflectivity: a ~10 to 12 km wide northern zone and a ~5 to 7 km wide southern zone, both about 5 km thick and 7 to 8 km below surface. We interpret the BMA source to be at least in part, a Namaqua-like massive to disseminated, deformed/metamorphosed stratiform sulphide-magnetite ore body with metasomatic overprint. The seismic reflection and -refraction data support an interpretation that a Pan-African suture zone at the BMA is absent and that instead, the NNMB continues below the CFB tectonic front, probably up to the continental margin and the Agulhas Fracture Zone. The seismic reflection data also supports a thin-skinned tectonic thrust model for the evolution of the CFB without significant fore-deep stratigraphic thickening of the Karoo Basin strata. A compatible tectonic model implies a Palaeozoic collision orogen setting, coupled to a south verging subduction zone much farther south of the CFB. Similarly, the geophysical data support a south dipping subduction zone during the amalgamation of the NNMB in the Mesoproterozoic. Current reconstructions of the Rodinia supercontinent link the NNMB and the Grenville Province of North America across the Grenville-Kibaran orogen. Our seismic section tests this reconstruction through a direct comparison with seismic profiles on the opposite flank of the orogen. Although the once adjacent continental blocks are now 1000s of kilometres apart, the seismic images show a good correlation and support the reconstruction.