Amphibians face an unknown future in a time of rapid environmental change due to global climate perturbations. Since amphibians are perceived to be indicators of ecosystem health, understanding the causes of their declines can improve our perception of threats to other species. Molecular techniques have allowed us to explore how environmental change affects genetic variation and to predict evolutionary adaptive potential of amphibian populations. The identification of populations with the greatest potential to respond to changing environmental variables may be an important conservation strategy to aid in future management efforts. I utilized targeted exon capture sequencing to identify adaptive variation in California tiger salamanders (CTS; Ambystoma californiense), a species threatened by land use change and hybridization with barred tiger salamanders (A. mavortium). I identified 17 and 26 outlier loci for balancing selection in historic and recent samples of CTS respectively. The outlier loci corresponded to genes of various functions, though none of the outliers associated significantly with the change in several tested environmental variables. Despite the lack of environmental correlations detected, it must also be considered that the outlier loci could be involved in epistatic interactions where many genes with small effects influence a single phenotype with fitness benefits. Additional hypotheses to explain the observed changes in allele frequencies and outliers may be the effects of UV-B radiation, pesticide use, or indirect effects of climate change.