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Through the local selection of landraces, humans have guided the adaptation of crops to a vast range of climatic conditions. This is particularly true of maize, which was domesticated in a restricted area of Mexico but now displays one of the broadest cultivated ranges. Here we combined reverse ecology and association mapping to study the molecular determinants of local adaptation along elevation gradients in teosintes, the closest wild relatives of maize. Our results revealed the phenotypic components of an altitudinal “syndrome”, with traits involved in spatially-varying selection. The proportion of outlier SNPs associating with phenotypic variation, however, was greatly affected by population stratification. Chromosomal inversions were enriched for phenotypically-associated SNPs. Altogether, our results are consistent with the set-up of an altitudinal syndrome promoted by local adaptation of teosinte populations in the face of gene flow. Interestingly local adaptation is also now occurring in Europe and benefits from adaptive introgression from maize.