Observing and counting bats is extremely difficult. Bats hide during the day, fly in darkness, and most species in the United States (US) become inactive and inaccessible in cryptic hibernation sites for 7-8 months each year. More than 40 different species of bats occur year-round in the US, yet reasonable population estimates exist for very few. Populations of US bats face new and unprecedented threats from white-nose syndrome (WNS) and industrial wind turbines. Like WNS, wind energy development might adversely affect entire populations of bats. Species of bats dying at wind turbines in the greatest numbers rank among the most cryptic, elusive, and poorly understood. Hoary bats (Lasiurus cinereus) compose approximately half of the tens to hundreds of thousands of bat fatalities estimated to occur each year in the US and Canada at wind turbines, dying disproportionately more than any other US bat species. This highly migratory species is found dead during late summer and autumn at most wind facilities where carcass monitoring occurs, yet conservation implications of hoary bat deaths at wind turbines remain as unknown as the size of their historical or current population is elusive.Much of what is known about populations of hoary bats comes from genetic studies. Prior studies used a variety of genetic markers to study: taxonomic relationships to other species, migratory origins, as well as estimating the history, size, and structure of hoary bat populations. These previous genetic efforts led to new understanding, yet each focused on relatively narrow glimpses of the hoary bat genome, sometimes creating uncertainty where clarity is needed from a resource-management perspective. High-throughput sequencing methods now give us the opportunity to quickly learn far more about cryptic bat populations, while concurrently developing new tools and answering previously intractable questions about bats, their prey, and their microbiome. Driven by the critical need for resource managers to better gauge the effects of wind turbines on hoary bats, we aim to rapidly expand understanding of their populations by using genomics to study the demographic history of hoary bats, and to generate gene models for understanding whether a major population decline may be occurring in hoary bats over the past decade.