The transition of a society from traditional to market-based diets (termed the nutrition transition) has been associated with profound changes in culture and health. We are developing biomarkers to track the nutrition transition in the Yup'ik Eskimo population of Southwest Alaska based on naturally occurring variations in the relative abundances of carbon and nitrogen stable isotopes (δ(15)N and δ(13)C values). Here, we provide three pieces of evidence toward the validation of these biomarkers. First, we analyzed the δ(15)N and δ(13)C values of a comprehensive sample of Yup'ik foods. We found that δ(15)N values were elevated in fish and marine mammals and that δ(13)C values were elevated in market foods containing corn or sugar cane carbon. Second, we evaluated the associations between RBC δ(15)N and δ(13)C values and self-reported measures of traditional and market food intake (n = 230). RBC δ(15)N values were correlated with intake of fish and marine mammals (r = 0.52; P < 0.0001). RBC δ(13)C values were correlated with intake of market foods made from corn and sugar cane (r = 0.46; P < 0.0001) and total market food intake (r = 0.46; P < 0.0001). Finally, we assessed whether stable isotope ratios captured population-level patterns of traditional and market intake (n = 1003). Isotopic biomarkers of traditional and market intake were associated with age, community location, sex, and cultural identity. Self-report methods showed variations by age and cultural identity only. Thus, stable isotopes show potential as biomarkers for monitoring dietary change in indigenous circumpolar populations.