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Based on joint consideration of S receiver functions and surface-wave anisotropy we present evidence for the existence of a thick and layered lithosphere beneath the Kalahari Craton. Our results show that frozen-in anisotropy and compositional changes can generate sharp Mid-Lithospheric Discontinuities (MLD) at depths of 85 and 150-200 km, respectively. We found that a 50 km thick anisotropic layer, containing 3% S wave anisotropy and with a fast-velocity axis different from that in the layer beneath, can account for the first MLD at about 85 km depth. Significant correlation between the depths of an apparent boundary separating the depleted and metasomatised lithosphere, as inferred from chemical tomography, and those of our second MLD led us to characterize it as a compositional boundary, most likely due to the modification of the cratonic mantle lithosphere by magma infiltration. The deepening of this boundary from 150 to 200 km is spatially correlated with the surficial expression of the Thabazimbi-Murchison Lineament (TML), implying that the TML isolates the lithosphere of the Limpopo terrane from that of the ancient Kaapvaal terrane. The largest velocity contrast (3.6-4.7%) is observed at a boundary located at depths of 260-280 km beneath the Archean domains and the older Proterozoic belt. This boundary most likely represents the lithosphere-asthenosphere boundary, which shallows to about 200 km beneath the younger Proterozoic belt. Thus, the Kalahari lithosphere may have survived multiple episodes of intense magmatism and collisional rifting during the billions of years of its history, which left their imprint in its internal layering.