Hoary bats are among the bat species most commonly killed by turbine strikes in the midwestern United States. The impact of this mortality on species census size is not understood, due in part to the difficulty of estimating population size for this highly migratory and elusive species. Genetic effective population size (Ne) could provide an index of census population size if other factors affecting Ne are stable. In support of this and other population-genetic studies, we analyzed two temporally spaced cohorts: 96 hoary bats collected in 2009-2010 and an additional 96 collected in 2017-2018. Samples consisted of wing clips removed from archived carcasses and were obtained by agreement from the U.S. Fish and Wildlife Service, the sponsor of this research. All carcasses were originally collected post mortem at wind-turbine facilities in the state of Indiana and subsequently frozen, although for our research purposes the collection location or cause of death is not material. We sequenced restriction-site associated polymorphisms and generated a de novo genome assembly to guide the removal of sex-linked and multi-copy loci, as well as identify physically linked markers. This data release includes the computationally inferred genotypes at 12,915 single-nucleotide polymorphisms (SNPs) for 186 individuals, after excluding six individuals with insufficient data. It also includes the reference genome sequence used to identify physically linked loci and remove sex chromosomes from analysis.