The northern North American Cordillera is a globally significant center of endemism. In western North America, arid steppe habitats support a number of unique species, including several endemic lichens. However, processes driving diversification and endemism in this region remain unclear. In this study, we investigate diversity and phylogeography of the threatened wanderlust lichens (mycobiont=Rhizoplaca species) which occur free on calcareous soils in steppe habitats in western North America. Wanderlust lichens comprise three species of lichen-forming fungi (LFF) – Rhizoplaca arbuscula, R. haydenii, and R. idahoensis (endangered, IUCN Red List) – which occur in fragmented populations in Idaho and Wyoming, with limited populations in southeastern Montana and northern Utah. These lichens reproduce almost exclusively via large, asexual vegetative propagules. Here, our aims were to (i) assess the evolutionary origin of this group, (2) investigate genetic diversity across populations throughout the distribution of these species, and (3) create species distribution models (SDMs) to better understand potential factors limiting distributions. Using a genome-skimming approach, we generated a 19.1Mb alignment, spanning ca. half of the complete LFF genome, from specimens collected throughout the entire range of wanderlust lichens. Based on this phylogeny we investigated phylogeographic patterns using RASP. Finally, we used MaxEnt to estimate SDMs for R. arbuscula and R. haydenii. We inferred a highly structured topology, with clades corresponding to distinct geographic regions and morphologies represented throughout the group’s distribution. We found that R. robusta, a sexually reproducing taxon, is clearly nested within this asexual lineage. Phylogeographic analyses suggest that both dispersal and vicariance played a significant role throughout the evolutionary history of the vagrant Rhizoplaca clade, with most of the dispersal events originating from the Salmon Basin in eastern Idaho – the center of diversity for this group. Despite the fact that vagabond lichens are dispersal limited due to large, unspecialized vegetative propagules, we inferred multiple dispersal events crossing the Continental Divide. Comparing herbarium records with SDMs suggests that vagabond lichens don’t fully occupy the areas of highest distribution probability. In fact, documented records often occur in areas predicted to be only marginally suitable. These data suggest a potential mismatch between contemporary habitats outside of the center of diversity in eastern Idaho with the most suitable habitat, adding to the vulnerability of this imperiled complex of endemic lichens.