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Biological soil crusts are foundational to natural ecosystem function in semi-arid regions of the world, including the Western U.S. They are composed of phyletically diverse organisms, including microbes, green algae, lichens, and mosses. While diminutive, these assemblages have a large ecological impact - for example, they stabilize soil, fix nitrogen, and store water, nutrients, and organic matter. Importantly, these functions facilitate the establishment of vascular plants. Biocrusts are extremely susceptible to mechanical disturbance and thus have been depleted throughout the semi-arid West. As a result, restoration of functional ecosystems in the West may often depend on the re-establishment of biocrust communities. However, successful restoration must anticipate often extreme environmental gradients, for example the decreasing intensity of monsoonal precipitation on the Colorado Plateau from the Mogollon Rim to the Uinta Basin. Such gradients are expected to select for locally adapted genotypes; consequently, materials for restoration should be sourced carefully to optimize restoration outcomes. Sourcing may be especially important for biocrust mosses, including the widely distributed�Syntrichia ruralis,�which are predominantly asexual and thus may be less able to respond to selection imposed at a restoration site or during materials development. To expand our basic knowledge of biocrusts and gain insight into how best to restore them, we used next-generation sequencing to genotype�Syntrichia ruralis�populations collected across the monsoonal gradient of the Colorado Plateau. We found that populations exhibit significant genetic differentiation, and present evidence that some of this differentiation may reflect local adaptation. The genetic techniques employed here provide a promising and cost-effective mechanism to characterize genetic differentiation and diversity of restoration species, and they may prove to be useful tools to guide future restoration efforts.