There is generally a dearth of evidence of the nature of Quaternary climate change within desert systems, which has limited precious interpretations of past environmental change at low latitudes. The Last Glacial Maximum has previously been identified as the peak of Late Quaternary aridity, when desert systems expanded to five times their present extent(1-3), and low-latitude aridity has been described for previous glaciations(4). But little evidence has been derived directly for large desert basins, particularly southern Africa. Here we report new chronological (optical dating) evidence of arid episodes recorded in aeolian sediments from the Mega Kalahari sand sea. Episodic aeolian activity is recorded at the northeastern desert margin, whereas more sustained activity is evident from the southwestern desert core. Several significant arid events are apparent since the last interglacial period, with dune-building (arid) phases at similar to 95-115, 41-46, 20-26 and 9-16kyr before present. Existing atmospheric general circulation model simulations and independent palaeoclimate data indicate that the changes in aridity are related to changes in the northeast-southwest summer rainfall gradient, which are in turn related to sea surface temperatures in the southeastern Atlantic Ocean.