The first fission track analyses of detrital apatite grains from the subsurface of the Kaapvaal Craton were utilized to delineate the thermal history for the northern margin of the Witwatersrand Basin, South Africa, where evidence for subsurface thermophilic and hyperthermophilic microorganisms have been discovered. Fission track apatite ages for core samples ranged from 21 to 422 Ma. The trend of decreasing age with increasing depth parallels a trend previously reported for fission track data from surface samples collected from the higher altitude centre and lower altitude margins of the Kaapvaal Craton, South Africa. These new fission track ages are older than the surface samples of equivalent elevation, indicating that the uplift history and/or the geothermal gradient of the centre of the Kaapvaal Craton is distinct from that of its margins. Modelling of one sample collected from a depth of 3.7 km records cooling from 120°C at 75 Ma at a rate of approximately 1.4°C m.y.−1 and reaching present day temperatures at 30 Ma. This modelling result when compared to other apatite fission track dates indicate that this cooling trend followed a 90-Ma thermotectonic event. The fission track data also indicate that heated fluid migration, which is observed today in this region of the Witwatersrand Basin, was also active in the past in order to explain the greater palaeogeothermal gradient (18 versus 8°C km−1). The fission track results suggest that at approximately 70 Ma only hyperthermophilic microorganisms could have existed at palaeodepths >3.2 km depth in the Witwatersrand Basin, and that the current meso/thermophilic microbial communities living at or beneath the present depth of 1.7 km in the Witwatersrand Basin must have migrated to their current location since 70 Ma. Any hyperthermophilic microorganisms found at the present depths 1.2–3.7 km could be descendents of subsurface hyperthermophiles that colonized the crust since the early Mesozoic to Palaeozoic eras.