Seismic anisotropy within the lithosphere of cratons preserves an important record of their ancient assembly. In southern Africa, anisotropy across the Archean Kaapvaal Craton and Limpopo Belt has been detected previously by observations of SKS-wave splitting. Because SKS-splitting measurements lack vertical resolution, however, the depth distribution of anisotropy has remained uncertain. End-member interpretations invoked the dominance of either anisotropy in the lithosphere (due to the fabric formed by deformation in Archean or Palaeoproterozoic orogenies) or that in the asthenosphere (due to the fabric formed by the recent plate motion), each with significant geodynamic implications. To determine the distribution of anisotropy with depth, we measured phase velocities of seismic surface waves between stations of the Southern African Seismic Experiment. We applied two complementary measurement approaches, very broad-band cross-correlation and multimode waveform inversion. Robust, Rayleigh- and Love-wave dispersion curves were derived for four different subregions of the Archean southern Africa in a period range from 5 s to 250–400 s (Rayleigh) and 5 s to 100–250 s (Love), depending on the region. Rayleigh-wave anisotropy was determined in each region at periods from 5 s to 150–200 s, sampling from the upper crust down to the asthenosphere. The jackknife method was used to estimate uncertainties, and the F-test to verify the statistical significance of anisotropy. We detected strong anisotropy with a N–S fast-propagation azimuth in the upper crust of the Limpopo Belt. We attribute it to aligned cracks, formed by the regional, E–W extensional stress associated with the southward propagation of the East African Rift. Our results show that it is possible to estimate regional stress from short-period, surface wave anisotropy, measured in this study using broad-band array recordings of teleseismic surface waves. Rayleigh-wave anisotropy at 70–120 s periods shows that the fabric within the deep mantle lithosphere of the Limpopo Belt and northern Kaapvaal Craton is aligned parallel to the Archean–Palaeoproterozoic sutures at block boundaries. This confirms that the fabric within the lithosphere created by pervasive ancient deformation is preserved to this day. Suture-parallel fabric is absent, however, in the deep lithosphere of the western Kaapvaal Craton, suggesting that it was not reworked in the collision with the craton’s core, either due to its mechanical strength or because the deformation mechanism was different from those that operated in the north. Anisotropy at periods greater than 120–130 s shows fast directions parallel to the plate motion and indicates shear wave anisotropy in the asthenosphere. The depth distribution of anisotropy revealed by surface wave measurements comprises elements of both end-member models proposed previously: anisotropy in the asthenosphere shows fast-propagation directions parallel to the plate motion; anisotropy in the Limpopo and northern Kaapvaal lithosphere shows fast directions parallel to the Archean–Palaeoproterozoic sutures. The distribution of SKS-splitting orientations across southern Africa reflects anisotropic fabric both within the lithosphere (dominating the splitting beneath the Limpopo Belt and northern Kaapvaal Craton) and within the asthenosphere (dominating beneath the western Kaapvaal Craton).