Teosintes, the wild relatives of maize, exhibit a wide ecogeographic distribution across Mexico and Central America, spanning starkly varying precipitation and temperatures. Understanding the genetic basis of teosinte’s adaptation to such conditions is crucial for its in situ conservation. We present findings from a study of 3,455 individuals across 276 teosinte populations, encompassing all known taxa except Zea vespertillio. Environmental and morphological data, along with genotype data comprising 33,929 SNPs, were analysed to elucidate the genetic population structure, ecological adaptation, and candidate genes associated with various climatic factors and phenotypic traits. Our results revealed distinct genetic and phenotypic adaptations within teosinte populations, shaped by the climate conditions of their habitats. Genome-wide association studies (GWAS) identified significant SNPs associated with morphological traits and environmental factors, elucidating adaptive mechanisms in teosinte evolution. Comparative analysis with maize literature on GWAS on SNPs found to be associated with agronomically important maize phenotypes highlighted both shared and unique genetic variants between teosinte and maize. Furthermore, protein function annotated to marker loci regions revealed the multifaceted nature of adaptive strategies in teosinte, indicating different potentially adaptive loci, even between populations growing in similar environmental conditions. Recognizing this diversity is important for teosinte conservation, as pointed out by new international frameworks, and for its management considering teosinte’s gene flow with maize, potential transgenic flow and the risk of new weeds emergence. Our research underscores the importance of studying the genetic diversity of crop wild relatives at the population level within centers of origin.