Proto-Indian craniometric identity established in India by the middle Holocene

India's largest assemblage of prehistoric hunter-gatherer burials was recovered from three related, Mesolithic sites in the Ganges Valley. Our recent craniometric documentation of six large samples of modern Indians provides the opportunity to investigate the similarity of 19 Mesolithic Ganges crania to modern Indians in the context of the 28 non-Indian series recorded by W.W. Howells. Most of the Mesolithic Ganges crania are incomplete and so they were analyzed individually and their classification results then summarized. Overall, eight classify as modern Indian, in a pattern whereby those with a larger number of measurements available for analysis, and with characteristically Indian cranial indices, are more likely to classify as Indian. In contrast, only a miniscule proportion of the crania measured by W.W. Howells classify as modern Indian. On that basis, the Mesolithic Ganges can be characterized as ‘proto-Indian’, and can be considered representative of a pre-agricultural population that made a major contribution to the phenotype of modern Indians. •Eight of 19 analyzed crania from mid-Holocene Mesolithic Ganges sites classify as Indian.•This pre-agricultural sample is similar to albeit distinguishable from modern Indians.•The represented population made a major contribution to later South Asians' phenotype.•A finding in line with genetic evidence on recent Indians' deep-rooted local ancestry.