The last two decades have seen important advances in our knowledge of maize domestication, thanks in part to the contributions of genetic data. Genetic studies have provided firm evidence that maize was domesticated from Balsas teosinte (Zea mays subspecies parviglumis), a wild relative that is endemic to the mid-to lowland regions of southwestern Mexico. An interesting paradox remains, however: Maize cultivars that are most closely related to Balsas teosinte are found mainly in the Mexican highlands where subspecies parviglumis does not grow. Genetic data thus point to primary diffusion of domesticated maize from the highlands rather than from the region of initial domestication. Recent archeological evidence for early lowland cultivation has been consistent with the genetics of domestication, leaving the issue of the ancestral position of highland maize unresolved. We used a new SNP dataset scored in a large number of accessions of both teosinte and maize to take a second look at the geography of the earliest cultivated maize. We found that gene flow between maize and its wild relatives meaningfully impacts our inference of geographic origins. By analyzing differentiation from inferred ancestral gene frequencies, we obtained results that are fully consistent with current ecological, archeological, and genetic data concerning the geography of early maize cultivation.T he geography of origins and diversification of agricultural species has important implications for unraveling the ecological context of Neolithic societies and for understanding current patterns of diversity in domesticated plants and animals. Traditionally the realm of archeology and botany (1, 2), the study of plant domestication has seen important contributions from genetics during the last two decades (3). Genetic data often provide evidence that is hard to obtain by other means, making it an invaluable complement to other lines of inquiry.As a case in point, molecular markers were instrumental in establishing the single domestication of maize (Zea mays subspecies mays) from an extant wild relative (4, 5). Maize was shown to originate from annual teosinte (Zea mays subspecies parviglumis, hereafter parviglumis) around 9,000 y B.P., placing domestication in the mid-to lowland regions of southwest Mexico where parviglumis grows endemically. As predicted by this result (6), excavations in the heart of parviglumis' distribution have produced the earliest (8,700 y B.P.) phytolith evidence for maize cultivation (7). Other finds from Tabasco (7,300 y B.P.) (8) and Panama (7,400 y B.P.) (9) also support an early presence of maize throughout the Meso-American lowlands.Although different types of evidence seemingly concur, questions nonetheless remain about the interpretation of the genetic data. While unequivocal with respect to maize's wild ancestor, marker evidence suggests that maize from the Mexican highlands, rather than from the lowlands, is most closely related to parviglumis and appears to have given rise to all cultivars currently grown throug...