The compositional structure and thermal state of the subcontinental lithospheric mantle (SCLM) beneath the Kalahari Craton and the surrounding mobile belts have been mapped in space and time using >3400 garnet xenocrysts from >50 kimberlites intruded over the period 520–80 Ma. The trace-element patterns of many garnets reflect the metasomatic refertilisation of originally highly depleted harzburgites and lherzolites, and much of the lateral and vertical heterogeneity observed in the SCLM within the craton is the product of such metasomatism. The most depleted, and possibly least modified, SCLM was sampled beneath the Limpopo Belt by early Paleozoic kimberlites; the SCLM beneath other parts of the craton may represent similar material modified by metasomatism during Phanerozoic time. In the SW part of the craton, the SCLM sampled by “Group 2” kimberlites (>110 Ma) is thicker, cooler and less metasomatised than that sampled by “Group 1” kimberlites (mostly ≤95 Ma) in the same area. Therefore, the extensively studied xenolith suite from the Group 1 kimberlites probably is not representative of primary Archean SCLM compositions. The relatively fertile SCLM beneath the mobile belts surrounding the craton is interpreted as largely Archean SCLM, metasomatised and mixed with younger material during Paleoproterozoic to Mesoproterozoic rifting and compression. This implies that at least some of the observed secular evolution in SCLM composition worldwide may reflect the reworking of Archean SCLM. There are strong correlations between mantle composition and the lateral variations in seismic velocity shown by detailed tomographic studies. Areas of relatively low Vp within the craton largely reflect the progressive refertilisation of the Archean root during episodes of intraplate magmatism, including the Bushveld (2 Ga) and Karroo (ca. 180 Ma) events; areas of high Vp map out the distribution of relatively less metasomatised Archean SCLM. The relatively low Vp of the SCLM beneath the mobile belts around the craton is consistent with its fertile composition. The seismic data may be used to map the lateral extent of different types of SCLM, taking into account the small lateral variations in the geotherm identified using the techniques described here.