Ecological restoration often requires translocating plant material from distant sites. Importing suitable plant material is important for successful establishment and persistence. Yet published guidelines for seed transfer are available for very few species. Accurately predicting how transferred plants will perform requires multi-year and multi-environment field trials and comprehensive follow-up work, and is therefore infeasible given the number of species used in restoration programs. Alternative methods to predict the outcomes of seed transfer are valuable for species without published guidelines. In this study, we analyzed the genetic structure of an important shrub used in ecological restorations in the Southern Rocky Mountains called alder-leaf mountain mahogany (Cercocarpus montanus). We sequenced DNA from 1440 plants in 48 populations across a broad geographic range. We found that genetic heterogeneity among populations reflected the complex climate and topography across which the species is distributed. We identified temperature and precipitation variables that were useful predictors of genetic differentiation and can be used to generate seed transfer recommendations. These results will be valuable for defining management and restoration practices for mountain mahogany.