["International Journal of Osteoarchaeology, EarlyView. ", "\nABSTRACT\nThis study uses nine Uralic‐speaking populations with documented multilayered genetic structure as a regional test case to evaluate how closely cranial nonmetric trait distances correspond to genetic differentiation and whether this correspondence varies across autosomal, mitochondrial, and Y‐chromosomal systems. Cranial nonmetric trait frequencies were summarized as phenotypic distances using the mean measure of divergence (MMD). Published distance matrices for autosomal, mtDNA, and Y‐chromosomal FST, together with geographic and lexical distances, were analyzed using Mantel and partial Mantel tests, multiple regression on distance matrices (MRM), and Procrustes superimposition of two‐dimensional PCoA configurations. In simple Mantel tests, MMD showed positive associations with all comparison matrices. Lexical distance exhibited the strongest unadjusted association, autosomal and mtDNA FST showed intermediate correspondence, and Y‐chromosomal FST and geographic distance showed weaker associations. When geographic distance was included as a covariate, associations with autosomal and mtDNA structure persisted, whereas correspondence with Y‐chromosomal variation was not supported. Across adjusted and multivariate analyses, autosomal FST showed the most consistent support in this sample. Procrustes comparisons revealed substantial concordance between MMD and autosomal configurations, weaker concordance with mtDNA, and no statistically supported concordance with Y‐chromosomal structure. Cranial nonmetric variation therefore shows differential concordance with genetic structure across marker systems: correspondence is strongest with genome‐wide autosomal differentiation, weaker and less consistent with mtDNA differentiation, and not robustly supported for Y‐chromosomal differentiation once geographic and lexical distances are included as covariates. These results indicate that cranial nonmetric traits can capture broad patterns of population affinity without providing a direct reconstruction of demographic mechanisms. From an osteoarcheological perspective, they remain a useful line of evidence for reconstructing regional population affinities when genetic data are incomplete, unavailable, or unevenly sampled.\n"]