Although significant environmental and climatic changes are likely to have occurred across the Pleistocene/Holocene transition in southern Africa, records are sparse, with information regarding temperature change especially rare. We thus know little about the conditions facing Later Stone Age human populations at this time, particularly those in the highland interior where temperature shifts would have had strong impacts on floral and faunal distributions. In Lesotho, a well-defined altitudinal distribution of C3 and C4 photosynthetic plant taxa, and their remains in soil organic matter, provides a means of estimating past temperature shifts. We applied this principle to stratified sediments from two archaeological sequences in the Lesotho lowlands (c. 1600 m a.s.l.) to produce a palaeotemperature record focusing on the period 14 000–9500 cal a BP. The results show an overall trend from exclusively C3 vegetation at the Last Glacial Maximum towards greater contributions of C4 taxa, and thus warmer conditions, during the Holocene. However, large temperature fluctuations are evident within this trend, with rapid changes of up to 4 °C visible between 11 200 and 9500 cal a BP. The continued presence of hunter-gatherers during this time suggests that the region must have remained attractive to human populations despite significant climatic instability and cool episodes. Copyright © 2013 John Wiley & Sons, Ltd.