While the distribution and ranges of arctic plants were greatly affected by the advance and retreat of ice sheets, the impact of glacial and interglacial cycles on lichenized fungi remains largely unexplored. In this study we examine the impact of Pleistocene climatic changes on two closely related Xanthomendoza (Teloschistaceae, Ascomycota) species with distinct distribution patterns and reproductive strategies. We selected X. borealis, which occurs in polar regions of both hemispheres, and the corticolous X. montana, which is restricted to montane shrublands in western North America. We analyzed the complete nuclear ribosomal internal transcribed spacer region (ITS) to confirm the monophyly and relative ages of X. borealis and X. montana. We estimated molecular diversity and population demographics statistics, mismatch distributions, and Bayesian skyline plots for both species. Our data indicate that X. montana experienced a Late Pleistocene population expansion. We suggest that major shifts in vegetation types as a result of Pleistocene climate change had a substantial impact on distribution patterns and the demographic history of X. montana. In contrast, results from this study indicate that the demographic history of X. borealis is consistent with long-term stability, although low genetic variability in the ITS marker for X. borealis limits overall confidence in this inference. We propose that X. borealis has been able to maintain a stable population size across climatic shifts, likely through effective dispersal to suitable habitats and suggests that climatic conditions during Pleistocene glacial cycles were not inherently unfavorable or restrictive for some high altitude/latitude lichen-forming fungal species. Investigating mating systems for these two Xanthomendoza species may provide important insights about the factors affecting population demographics and reproduction in lichen-forming fungi in general.