Studies investigating evolutionary theories on the origins of national differences in intelligence have been criticized on the basis that both national cognitive ability measures and supposedly evolutionarily informative proxies (such as latitude and climate) are confounded with general developmental status. In this study 14 Y chromosomal haplogroups (N=47 countries) are employed as evolutionary markers. These are (most probably) not intelligence coding genes, but proxies of evolutionary development with potential relevance to cognitive ability. Correlations and regression analyses with a general developmental indicator (HDI) revealed that seven haplogroups were empirically important predictors of national cognitive ability (I, R1a, R1b, N, J1, E, T[+L]). Based on their evolutionary meaning and correlation with cognitive ability these haplogroups were grouped into two sets. Combined, they accounted in a regression and path analyses for 32–51% of the variance in national intelligence relative to the developmental indicator (35–58%). This pattern was replicated internationally with further controls (e.g. latitude, spatial autocorrelation etc.) and at the regional level in two independent samples (within Italy and Spain). These findings, using a conservative estimate of evolutionary influences, provide support for a mixed influence on national cognitive ability stemming from both current environmental and past environmental (evolutionary) factors.