We estimated that Iberian ancestry composes as much as a third of the European ancestry in Latinos in Florida, New Mexico, and other parts of the Southwest, probably reflecting either early Spanish influence and rule in these regions or recent immigration from Latin America, which might also be associated with higher levels of Iberian ancestry in New York and New Jersey. Regions with higher Iberian ancestry also correspond to regions with greater Native American ancestry; disentangling whether higher levels of Native American ancestry in the Southwest reflects the legacy of indigenous Native American ancestors or is the result of recent Latino immigrants into the Southwest might be possible through future studies of admixture dating or more Native American subpopulation reference data.