Mexico’s topographic and environmental heterogeneity, in combination with environmental fluctuations of the Neogene-Quaternary, has uniquely influenced the evolutionary history and distribution patterns of the region’s flora and fauna, sometimes causing closely related species to exhibit distinct climatic niches. Our study aimed to characterize the climatic niches of Thamnophis scalaris and Thamnophis scaliger, as well as evaluate the impact of the Pleistocene-Holocene transition on their paleodistributions. We generated 357 models per species, each with three sets of distinct combinations of climatic variables, based on 108 occurrence records for T. scalaris and 62 for T. scaliger. We evaluated the niche overlap, equivalency, and similarity between both species and transferred the present-day models to eight distinct historical periods, with the goal of encompassing the distinctive climatic variation of the Pleistocene-Holocene (P-H) transition. Both species showed significant differences in their respective climatic regimes and did not display climatic niche conservatism (the tendency of species to retain ancestral ecological characteristics), despite their previously reported ecological, morphological, and biogeographic similarities. Likewise, they seem to have responded similarly to the environmental changes in the P-H, with both paleodistributions experiencing expansion phases during glacial periods and contraction phases during interglacial periods. Possible areas of refugia that remained climatically stable and viable for both species throughout this period were identified. These refugia could potentially harbor a greater genetic diversity with respect to regions that recently acquired suitable conditions for the establishment of these populations. As such, this work offers a methodological procedure that may be used as an early inference for identifying specific regions of interest in phylogeographic studies and conservation planning.