Bats are vital to healthy ecosystems, providing billions of dollars of services in the form of forest and crop pest control. Unfortunately, North American bat populations have faced novel pressures during the past decade that may threaten their persistence. First, several species of tree-roosting bats (primarily hoary [Lasiurus cinereus], eastern red [L. borealis], and silver-haired [Lasionycteris noctivagans] bats) are experiencing large numbers of fatalities at industrial wind-energy facilities. Second, several species of cave-dependent bats have experienced large-scale mortality as the result of infection by a fungal pathogen that causes white-nose syndrome (WNS). As bats are generally long-lived and have low reproductive rates, such increases in mortality can cause significant population declines from which they may be unable to recover. Basic questions about population trends, size and structure remain largely unanswered for these species because of challenges in applying traditional wildlife monitoring approaches to bats. This lack of understanding impedes conservation and management efforts. In my dissertation, I use genomic and acoustic survey techniques to investigate questions related to the threats that wind-energy development and WNS are posing to bat species in North America. In my first chapter, I evaluate range-wide population structure and effective population size (Ne) for hoary, eastern red, and silver-haired bats. Using genotyping-by-sequencing (GBS), I genotyped single-nucleotide polymorphism (SNP) data from 173 hoary, 113 eastern red, and 89 silver-haired bats from multiple locations spread across their geographic distributions. Hoary bats and eastern red bats showed no geographic structure in genetic diversity, whereas silver-haired bats displayed longitudinal population variation. Coalescent modeling suggested that eastern red bats have the largest evolutionary Ne, followed by hoary bats, then silver-haired bats. In my second chapter, I used GBS to assess the population structure of two federally endangered cave bat species: Indiana bats (Myotis sodalis) and gray bats (M. grisescens). Using tissue samples from 45 Indiana bats and 47 gray bats spread across their ranges, I showed that Indiana bats display no geographic genetic structure, whereas gray bats exhibit east–west population variation across the Mississippi River Valley. In my final chapter, I used acoustic surveys across the State of Maryland to investigate bat community changes in the decade following the arrival of WNS. From 2010 through 2019, I conducted annual mobile acoustic routes each summer, for a total of 344 completed routes resulting in 426 hours of recordings and 24,375 identified bat passes. I detected massive (> 92%) declines of little brown bats (M. lucifugus), northern long-eared bats (M. septentrionalis), eastern small-footed bats (M. leibii), and tricolored bats (Perimyotis subflavus), with no evidence of recovery in recent years. Trends in hoary bats and eastern red bats were non-significant during this period. Bat community composition varied among Maryland’s physiographic regions, with eastern red bats comprising a larger percentage in the east. Species composition across the state likely reflects the impact of several factors, including mortality from WNS and wind-energy development, and perhaps reduced interspecific competition. Overall, my results illustrate the unique insights, but also distinct limitations, that genomic and acoustic data can provide regarding the conservation of bats in North America.