Rayleigh wave phase velocity maps in southern Africa are obtained at periods from 6 to 40 s using seismic ambient noise tomography applied to data from the Southern Africa Seismic Experiment (SASE) deployed between 1997 and 1999. These phase velocity maps are combined with those from 45 to 143 s period which were determined previously using a two-plane-wave method by Li & Burke. In the period range of overlap (25–40 s), the ambient noise and two-plane-wave methods yield similar phase velocity maps. Dispersion curves from 6 to 143 s period were used to estimate the 3-D shear wave structure of the crust and uppermost mantle on an 1°× 1° grid beneath southern Africa to a depth of about 100 km. Average shear wave velocity in the crust is found to vary from 3.6 km s–1 at 0–10 km depths to 3.86 km s–1 from 20 to 40 km, and velocity anomalies in these layers correlate with known tectonic features. Shear wave velocity in the lower crust is on average low in the Kaapvaal and Zimbabwe cratons and higher in the surrounding Proterozoic terranes, such as the Limpopo and the Namaqua-Natal belts, which suggests that the lower crust underlying the Archean cratons is probably less mafic than beneath the Proterozoic terranes. Crustal thickness estimates agree well with a previous receiver function study of Nair et al.. Archean crust is relatively thin and light and underlain by a fast uppermost mantle, whereas the Proterozoic crust is thick and dense with a slower underlying mantle. These observations are consistent with the southern African Archean cratons having been formed by the accretion of island arcs with the convective removal of the dense lower crust, if the foundering process became less vigorous in arc environments during the Proterozoic.