We assess craniometric variation in 153 individually dated human crania from South Africa with the aim of investigating genetic continuity/discontinuity during the Holocene. Evidence from the archaeological record is used to pinpoint likely episodes of genetic discontinuity. Craniometric data are then used to assess the likelihood of genetic change having occurred. Two periods of possible genetic discontinuity are identified: i) c. 4,000 BP, when an increase in overall population size, shifts in site organization and diet, and reduced mobility, were accompanied by reductions in stature; ii) c. 2,000 BP, when the herding of domesticates and the use of pottery vessels were introduced into the region. Results indicate that there was a decrease in cranial size and concomitant size-related changes in craniofacial shape between c.4,000 BP and 3,000 BP. This was followed almost immediately by a recovery in craniofacial size and a return to pre-4,000 BP craniofacial shape at c. 3,000 BP. This recovery continued gradually, extending into the herder period without any major shifts in morphology at 2,000 BP. It is suggested that the fluctuations in craniofacial size/shape were related to changes in environmental factors. Results obtained are consistent with long term continuity in South African Later Stone Age populations during the Holocene. Am J Phys Anthropol, 2007. © 2007 Wiley-Liss, Inc.