In the past years, several plant breeding programs have been done to select outstanding genotypes of sideoats grama (Bouteloua curtipendula) for restoration purposes. Such programs have been focused mainly on agronomic traits; however, little attention has been paid to the genetic structure and environmental adaptation of the selected genotypes. Thus, in this study we evaluated the genetic structure of 85 sideoats grama populations in Mexico. In addition, we modeled the past, present and future environmental niche of the genetic clusters of this species. Ninety sideoats grama populations were genetically analyzed through AFLP (Amplified Fragment Length Polymorphisms) markers. The environmental niche of the population clusters was modeled by using the maximum entropy method. The genetic analysis separated the populations into two genetically different clusters (p = 0.0003). The differentiation of these lineages can be partially explained by the paleoclimatic events experienced during the last interglacial and glacial maximums. Consequently, the genetic clusters have different environmental niche at the present time. Suitability areas for the distribution of Cluster I are mainly located in the central part of the country while the environmental niche of Cluster II is located in the semiarid region, close to the mountain range of the Sierra Madre Occidental. Thus, selection and restoration programs with sideoats grama must be carried out using local germplasm from each environmental niche. Given the environmental niche of both genetic clusters will suffer changes in the near and mid-century future, climate change must be considered for genotypes selection and restoration programs.