Local adaptation is common in widespread conifer species and current reforestation policy reflects this through local seed sourcing and breeding programs. However, as the climate changes local tree populations may become mismatched to their local environments. Our goal is to identify the genes responsible for climatic adaptation in western Canada’s two most economically important conifers, lodgepole pine (Pinus contorta) and interior spruce (Picea glauca, P. engelmannnii, and their hybrids). As the genomes of these species are very large (>20Gb), we have used sequence capture methods to target our sequencing efforts to regions of interest. To identify these regions, we developed a de novo transcriptome for each species and conducted an RNAseq expression study. Using these data and early drafts of the white spruce genome (SMarTForests Project) and the loblolly pine genome (PineRefSeq Project) we developed sequence capture probes for exons in >28K genes in lodgepole pine, and for >35K genes in interior spruce. Over 600 seedlings per species have been re-sequenced for these exons as well as for control, non-coding regions. We have sequenced these same individuals using a genotype-by-sequencing approach. Associations between provenance climate, phenotypes and SNP genotypes are being used to identify the climatic drivers of local adaptation in both species. Our results will be important for designing reforestation policies that consider future climates, and for understanding the genetic capacity of natural populations to rapidly adapt to new climatic conditions.