Introduction. The formation of the gene pool of modern Khakas people occurred through the interaction of various groups of ancient inhabitants of the Minusinsk Basin. This article is focused on the inter-group analysis of craniological series representing different Khakassian subethnic groups. Materials and Methods. The cranial series of the Kachins, Koibals, Sagais, and Beltirs was studied using the battery of 36 cranial non-metric characteristics. The obtained data was compared with data on other populations of Southern and Western Siberia: Shors, Tuvans, Telengits, Selkups, Khants, and Mansis. The analysis of the biological diversity of populations was carried out using Smith's mean measure of divergence (MMD) followed by multidimensional scaling and cluster analysis. Results. The Kachins are the most distant from the other Khakas subethnic groups, forming a cluster with the Telengits and Tuvans. The Koibals and Beltirs were positioned quite close to the Shors. The Sagais occupied a separate position in the Khakas cluster, presumably due to a greater proportion of Europoid admixture compared to other Khakas groups. The pooled Khakas sample shares similar cranial non-metric characteristics with Turkic-speaking ethnic groups of Southern Siberia: Shors, Telengits, and Tuvans. Discussion. The nature of phenetic differentiation of the Khakas sub-ethnic groups presumably reveals their complex population history. The position of the Kachins outside the Khakas cluster based on non-metric traits resulted from specificity of their phenofund, which is also supported by molecular genetic data. The similarity in the phenofund of the Khakas groups to those of the Tuvans and Telengits may result from gene flow between Khakas populations and the peoples of Southern Siberia or/and from their common episodes in their ethnogenesis. The similarity between pooled Khakassian sample and the Shors presumably suggests involvement of common genetic components in the gene pools of these peoples, which is consistent with molecular genetic data. Conclusion. The correspondence of the obtained results with genetic data suggests the possibility of using cranial non-metric traits to identify genetic relationships between ancient populations in the absence of direct genetic information.
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