Anthropogenic climate change in the western U.S. involves increasing temperatures, decreasing water availability and increasing frequency of extreme weather events. Predicting how subalpine forests will respond to climate change is complicated by variation in intraspecific responses. To address the question of whether subalpine tree populations will be able to tolerate future climatic conditions within their current distribution, I compared the physiological, phenological and morphological response of seedlings of two limber pine (Pinus flexilis James) mitochondrial haplotypes (narrow and wide-ranging) to simulated climate change. I conducted a 15-week growth chamber experiment on seedlings under low light conditions and two temperature treatments: ambient (recent climate conditions) and heated (ambient +5°C). I recorded the timing of developmental stages and measured seedling net photosynthetic and dark respiration rates, total biomass, root to shoot mass and length, specific leaf area (SLA) and specific root length (SRL). I found that the ambient chamber had greater average rates of net photosynthesis and dark respiration. Between haplotypes, there was a marginally significant difference in net photosynthesis and a significant difference in dark respiration. There were significant morphological differences between the haplotypes and chambers in root to shoot mass and SLA. Seedlings in the heated chamber germinated, on average, two weeks earlier than in the heated chamber and experienced a five-fold increase in mortality rate. The results of this experiment suggests that limber pine seedlings growing in the shade in a 5°C warmer climate will suffer near zero carbon balance, increased mortality, and will experience a longer growing season.