Natural tree populations consist of individuals that exhibit intraspecific adaptive variation at a range of geographic scales, as a result of the balance between gene flow and selection. The spatial distribution and magnitude of such variation will influence the capacity of populations to adapt to forthcoming changing environmental conditions. The native Scots pine populations in Scotland represent what remains of the iconic Caledonian forest. Despite being distributed within a relatively narrow geographic area these populations occur across a steep East-West environmental gradient of increasing rainfall and temperature. We hypothesised that western populations compared to those from the east may be better adapted to warmer conditions and as a consequence, may respond differently to the increased temperature predicted during climate change. We conducted an experiment lasting 22 weeks in controlled environment chambers using a nested hierarchical design based on material from different regions (west or east), populations and families (half sibs). We examined the effects of two temperature scenarios, current temperature and warmer predicted temperature on percentage germination as well as growth and morphology of above and below-ground traits. Most of the variation occurred at the family level. Nevertheless, significant regional and population differences were detected, where eastern populations invested more in roots, exhibited fewer stomatal rows per needle and produced thinner roots. In addition, warmer temperatures had strong effects on early growth that were consistent in material from both regions and resulted in earlier germination, greater growth and biomass, but these effects were not accompanied by shifts in biomass partitioning. Although the strong effect of warming suggested temperature limitation for early growth in the study areas under current conditions our results did not support the idea that low seedling recruitment resulting from poor emergence and early growth would lead to a decline in Scottish populations of Scots pine under a warmer climate. Our results are informative regarding the adaptive potential in the populations and will contribute to the development of appropriate forest conservation strategies.