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Admixture is a potential source of confounding in genetic association studies, so it becomes important to detect and estimate admixture in a sample of unrelated individuals. Populations of African descent in the US and the Caribbean share similar historical backgrounds but the distributions of African admixture may differ. We selected 416 ancestry informative markers (AIMs) to estimate and compare admixture proportions using STRUCTURE in 906 unrelated African Americans (AAs) and 294 Barbadians (ACs) from a study of asthma. This analysis showed AAs on average were 72.5% African, 19.6% European and 8% Asian, while ACs were 77.4% African, 15.9% European, and 6.7% Asian which were significantly different. A principal components analysis based on these AIMs yielded one primary eigenvector that explained 54.04% of the variation and captured a gradient from West African to European admixture. This principal component was highly correlated with African vs. European ancestry as estimated by STRUCTURE (r²=0.992, r²=0.912, respectively). To investigate other African contributions to African American and Barbadian admixture, we performed PCA on ～14,000 (14k) genome-wide SNPs in AAs, ACs, Yorubans, Luhya and Maasai African groups, and estimated genetic distances (F_ST). We found AAs and ACs were closest genetically (F_ST=0.008), and both were closer to the Yorubans than the other East African populations. In our sample of individuals of African descent, ～400 well-defined AIMs were just as good for detecting substructure as ～14,000 random SNPs drawn from a genome-wide panel of markers. Genet. Epidemiol. 34:561–568, 2010.? 2010 Wiley-Liss, Inc.