Landraces (traditional varieties) of crop species are a reservoir of useful genetic diversity, yet remain untapped due to the genetic linkage between the few useful alleles with hundreds of undesirable alleles1. We integrated two approaches to characterize the genetic diversity of over 3000 maize landraces from across the Americas. First, we mapped the genomic regions controlling latitudinal and altitudinal adaptation, identifying 1498 genes. Second, we developed and used F-One Association Mapping (FOAM) to directly map genes controlling flowering time across 22 environments, identifying 1,005 genes. In total 65% of the SNPs associated with altitude were also associated with flowering time. In particular, we observed many of the significant SNPs were contained in large structural variants (inversions, centromeres, and pericentromeric regions): 29.4% for flowering time, 58.4% for altitude and 13.1% for latitude. The combined mapping results indicate that while floral regulatory network genes contribute substantially to field variation, over 90% of contributing genes likely have indirect effects. Our strategy can be used to harness the diversity of maize and other plant and animal species.