Mexico is a center of diversification for the genus Quercus, with an important number of taxa occurring along the Trans-Mexican Volcanic Belt (TMVB). However, the impact of the interaction between historical and current climatic variation and geological heterogeneity in the TMVB on the genetic and phenotypic diversification within oak species has been scarcely investigated. We used chloroplast DNA microsatellites and a geometric morphometrics analysis of leaf shape to understand differentiation between populations of Quercus deserticola Trel., which inhabits dry highlands along the TMVB. Ecological niche modeling for present-day conditions and projections into past scenarios were performed to evaluate the influence of environmental variables on the evolutionary history of the species. Results showed high genetic diversity (hS= 0.774) and high genetic structure (RST= 0.75) and the morphological subdivision of populations into two clusters, corresponding to the west/south and east/north sectors of the Q. deserticola geographic distribution. Ecological niche modeling indicated that the potential distribution of the species has remained similar from the late Pleistocene to the present. Seemingly, the phylogeographic structure of the species has been shaped by low seed-mediated gene flow and mostly local migration patterns. In turn, leaf shape is responding to climate differences either through phenotypic plasticity or local adaptation.