The role of the tropics in global climate change is actively debated, particularly in regard to the timing and magnitude of thermal and hydrological response. Continuous, high-resolution temperature records through the Last Glacial Maximum (LGM) from tropical oceans have provided much insight but surface temperature reconstructions do not exist from tropical continental environments. Here we used the TEX86 paleotemperature proxy to reconstruct mean annual lake surface temperatures through the Last Glacial Maximum (LGM) in Lake Malawi, East Africa (9º-14ºS). We find a ~3.5ºC overall warming since the LGM, with temperature reversals of ~ 2ºC during the Younger Dryas (12.5 ka BP) and at 8.2 ka BP. Maximum Holocene temperatures of ~29ºC were found at 5 ka BP, a period preceding severe drought in Africa. These results suggest a substantial thermal response of southeastern tropical Africa to deglaciation and to varying conditions during the Holocene. The dataset is a paleotemperature reconstruction of mean annual surface temperature from the north basin of Lake Malawi, East Africa using the TEX86 paleothermometer. (TetraEther indeX of tetraethers with 86 carbon atoms). The age model for these cores is already available for previous Lake Malawi MP98 data sets on this website. TEX86 values are means of replicate analyses. All samples were measured at least in duplicate, half of samples were measured at least in triplicate. The calibration equation used to calculate mean annual lake surface temperatures (LST) is LST=(TEX86-0.25)/0.017 with a calibration error of +/- 2 degrees C. Lake Malawi core M98-1P: 10º15.9'S, 34º19.1'E, water depth 403m. Lake Malawi core M98-2P: 9º58.6'S, 34º13.8'E, water depth 363m. Lake surface elevation 474m.