Active management is needed to sustain healthy limber pine (Pinus flexilis E. James) forests in the Southern Rocky Mountains (henceforth, Southern Rockies), as they are threatened by the interaction of the mountain pine beetle (Dendroctonus ponderosae Hopkins) epidemic, climate change, and the spread of the non-native pathogen that causes white pine blister rust disease (Cronartium ribicola A. Dietr.). Appropriate source material for restoration and proactive introduction needs to be selected, taking into account potential genetic differentiation that would hamper management success. We conducted a common garden study in a greenhouse to determine the degree of genetic differentiation among limber pine populations in the Southern Rockies. We evaluated the differential responses of populations from northern and southern portions of the Southern Rockies to different moisture regimes during early seedling growth by measuring primary needle length, stem diameter, water potential, biomass allocation between root and shoot, and carbon isotope ratios (_δ13C; a proxy for water-use efficiency). There were significant (p < 0.05) effects of source region for root length, stem diameter, needle length, and total dry mass, with seedlings from southern sources bigger than seedlings from northern sources. Furthermore, there was a marginally significant interaction between soil moisture regime and source region for carbon isotope ratio (p = 0.0778), suggesting possible local adaptation. These data indicate that genetic differentiation exists among populations in the Southern Rockies, potentially increasing the risk of maladaptation when moving seed far from its source for active management.