The sample of South African early to mid-Holocene Later Stone Age (LSA) human crania is small and quite fragmentary, limiting our knowledge of human craniofacial morphology for this period. Previous limited analyses have described the morphology displayed by these early crania as a combination of Khoesan and non-Khoesan traits. Although essentially Khoesan-like in terms of facial morphology, their overall large size and robust neurocranial structure were regarded as atypical of Khoesan craniofacial morphology, leading to questions about the role of these early populations in the ancestry of recent Khoesan populations. Here we provide a quantitative analysis in which we compare five well-preserved pre-5000 BP LSA crania with (i) a large sample of post-5000 BP LSA Khoesan crania; and (ii) a sample of crania from recent South African Bantu-speakers. We show that these pre-5000 BP crania fall comfortably within the range of variation observed for the post-5000 BP Khoesan sample, in terms of both size and shape, suggesting that distinctive Khoesan craniofacial morphology was already present in South African LSA populations by the first half of the Holocene
