Conservation successes for the endangered Indiana bat (Myotis sodalis) in the early 2000s were largely reversed by white-nose syndrome (WNS), a novel fungal disease that emerged in North America in 2006. Impacts have been variable among Indiana bat colonies, but many maintain negative population growth, leading to concern for their long-term viability. Adaptive evolution (i.e., evolutionary rescue) could allow populations to persist despite disease, as has happened for other species; however, the evolutionary potential of Indiana bats remains unclear. Here, we perform a genome-wide scan to test for signatures of selection by comparing bat tissue samples from five geographic regions before and after WNS emergence. We tested for three types of selection across geographic scales: 1) selection targeting different genetic loci in different geographic regions; 2) parallel selection targeting similar loci range-wide; and 3) parallel selection affecting subsets of geographic regions. Our results suggest widespread evidence for selection in Indiana bats that varies by geographic region, implying differences in standing genetic variation or context-dependent WNS responses. We provide evidence for stabilizing and directional selection acting within individual geographic regions and in parallel within subsets of geographic regions. However, we detected no evidence of parallel selection acting on the same genomic coordinates across all geographic regions. Taken together, our results suggest selection in Indiana bats is driven in part by environmental factors that vary by geographic region or hibernaculum in addition to WNS.