The characterization of natural genetic diversity and the exploration of its relationship with variation in phenotypic traits is of great interest for evolutionary, conservation, and improvement purposes; in addition, understanding the relationships between genotype, phenotype, and the environment can provide insight on the molecular pathways controlling quantitative traits, as well as their fitness implications. The following work entails the characterization of a comprehensive panel of maize landraces from Latin America and is divided in 5 sections. The chapter "Identifying the diamond in the rough: a study of allelic diversity underlying flowering time adaptation in maize landraces" describes the general experimental design used to characterize the landrace panel. In this chapter the relationship between large scale altitude and latitude adaptation is also explored, and the trait flowering time is used as a case study to explore the genetic architecture of a complex trait through field experiments. The chapter "Genome-environment association allows identifying useful adaptive alleles from maize landraces" explores further the relationship between the genotypic variation in landraces and their adaptation to local abiotic environmental conditions. Because landraces have evolved for thousands of years in those environments, we observe significant association at candidate genes and observed that adaptive alleles are common and shared across populations, which has important consequences for future breeding efforts. The chapter "Genome wide association for plant height variation in maize landraces" represents the analysis of the genetic basis of plant height variation in landraces. Plant height, like yield, is a very complex trait with a significant heritable component. The association at key hormonal regulators, as well as flowering time associated regions, shows the potential to unveil genes underlying this trait, however the results of phenotypic prediction suggest that higher marker density is necessary to study traits on this order of complexity in a panel of very diverse landraces. The chapter "Exploring the potential for finding sources of resistance to Fusarium ear rot among maize landraces" represents the analyses of phenotypic evaluation of inoculated ear rot trials. Lastly, the final chapter "Integration of controlled populations and association mapping to score cytological features in the maize genome" describes the joint analyses of a mapping population segregating for the abnormal chromosome 10 and the landraces accessions. By combining the results of both populations, putative calls are made in the landraces regarding their chromosome 10 allele.