Climate change is becoming an ever-increasing issue for conservation efforts, especially in dryland ecosystems where natural resources are already scarce for native species. This is increasingly true for native amphibians in the area, which are already experiencing threats to their range by human intervention, disease, and invasive species. The objectives of this study are to 1) identify how climate change impacts the distribution of native and non-native amphibian species and high priority conservation areas (HPCA) in the drylands of the Southwest United States and northern Mexico; 2) Describe the relationship between environmental variables and spatial configurations of HPCA; 3) Explore how amphibians distributions and HPCA may respond under climate change scenarios; 4) Investigate the projected change in drivers of climate change; 5) Investigate how climate change will impact the critical areas for conservation of native amphibians. Distribution maps were obtained for the 220 resident native and non-native amphibian species, and complementarity-based analysis was used to identify HPCA for amphibians. We used 34 predictor variables grouped into three categories, and ranked based on their influence in determining HPCA. Finally, Zonation, species richness, and rarity-weighted richness (RWR) were evaluated to identify complementarity to HPCA. Results show that water-related variables and -related variables such as temperature and solar radiation were the best indicators of amphibian conservation HPCA. Zonation also proved to be the best method for identifying these HPCA. This study is the first to investigate the impact of climate change on site complementarity. The results from this study will open new inquiries for biogeography and conservation biology and also have a functional use for natural resource managers in the United States and Mexico to monitor changes to these areas and plan for recovery if needed.