Objective. To test the hypothesis that assortative mating for physical characteristics differs before and after major secular increases in height in an indigenous community in the Valley of Oaxaca, Mexico. Methods. Spouse pairs were identified in household and anthropometric surveys of a Zapotec-speaking community in 1978 (n = 68-70 pairs) and 2000 (n = 99-100 pairs). Height, weight, arm circumference, triceps skinfold and grip strength were measured. Assortative mating was calculated as Pearson correlations. Results. Husband-wife correlations for age were high in both years (r = 0.96, 0.95). Assortative mating for height was significant in 1978 (r = 0.35, p < 0.001) and in 2000 (r = 0.21, p < 0.01), but decreased when ages were controlled (1978, 0.21, p < 0.05; 2000, 0.11). Correlations (zero and second order, respectively) were low for the BMI (1978, 0.02, 0.02; 2000, 0.04, 0.05). Spouse correlations for grip strength were significant in both surveys (r = 0.25 to 0.45), but were reduced (p > 0.05) when ages of spouses were controlled (r = -0.02 to 0.16). Conclusion. Assortative mating for physical characteristics did not differ between surveys conducted before (1978) and after (2000) major secular increases in height in the community, and any possible genetic effect of the secular trend on assortative was likely negligible.