Genomic analysis of ancient crop samples provides opportunities to more precisely characterize the evolutionary history of plants and to connect this with patterns of human-assisted migration. Da Fonseca et al. sequenced DNA extracts from 32 archaeological maize samples dated from 700–6,000 years ago, from the Southwest of the United States and Mexico, as well as modern maize isolates. Their analyses resolve conflicting hypotheses from previous studies about the origin of maize in the Southwestern United States, providing support for initial dissemination following a highland route about 4,000 years ago, prior to gene flow with maize from the Pacific coast about 2,000 years ago.