We assessed whether morphological variability in populations of Pituophis deppei is related to the ecogeographic conditions of the biogeographic provinces they inhabit. This study includes four biogeographic provinces where the Mexican Pine Snake is reported: the Mexican Plateau, the Trans-Mexican Volcanic Belt, the Sierra Madre Occidental, and the Sierra Madre Oriental, Mexico. Specimens from the four biogeographic provinces were selected to analyze ecogeographic and morphological variation in the Mexican Pine Snake. A total of 789 occurrence records and 20 climatic and environmental variables were used to evaluate the overlap, conservatism, and divergence of ecological niches among the four provinces using an ecological niche model (ENM) for each one. Morphological variability was analyzed using geometric morphometrics with linear and discrete data from 262 specimens. The ENM results indicate that the distribution area of P. deppei is subdivided into four well-defined regions of habitat suitability associated with the Mexican Plateau, the Trans-Mexican Volcanic Belt, the Sierra Madre Oriental, and the Sierra Madre Occidental, with contact zones at their borders. These results indicate low overlap among the four provinces. Niche conservatism and niche divergence were supported by three and two pairwise comparisons, respectively. At the morphological level, linear morphometrics, scutellation, and black spot pattern accounted for enough variability to discriminate the specimens found in the Trans-Mexican Volcanic Belt from those of the other three provinces. As expected, the pattern of variation in head shape consists of well-defined character states exclusive to each of the four provinces inhabited by P. deppei. All the comparisons from the multivariate analyses of variance of landmark configurations with CVA were statistically significant, and the rates of correct posterior classifications were all above 35.5%. The ecogeographic variables used show reduced explanatory and predictive power for the variation in the morphological characters analyzed. The morphological variation in P. deppei could result from factors not considered in the present study, such as differences in trophic ecology, limited gene flow, non-adaptative variation, or phylogeographic implications. In the latter case, the morphological results obtained are consistent with one southern lineage previously reported using the haplotype configuration of species of P. deppei. Finally, our geometric morphometric approach allowed us to analyze head shape variability in P. deppei.