Migratory tree bats comprise the majority of casualties at wind energy facilities across North America and some species, like Lasiurus borealis, are suspected to be in decline. We took advantage of the large numbers of L. borealis and L. cinereus salvaged during fall migration at 1 wind farm in Texas and 3 wind farms in Minnesota to evaluate the ability of current genetic methods to estimate population size and detect genetic bottlenecks in these species. Using DNA extracted from wing membrane tissue samples, we genotyped 439 L. borealis and 246 L. cinereus at 6 microsatellite loci and a 550bp segment of the mitochondrial COI gene. Both microsatellite loci and mitochondrial haplotypes showed high levels of genetic diversity in each species. Historical estimates of Ne were large for both species. Estimates of NEf from the COI gene were almost 2 times higher for L. borealis than L. cinereus, whereas estimates utilizing microsatellite heterozygosity were higher for L. cinereus. We found a strong signal of rapid historical population growth and range expansion in L. borealis, but not in L. cinereus. The majority of our estimates of current Ne had upper 95% confidence intervals that encompassed infinity. There is some indication from contemporary estimates of Ne that L. borealis may have a lower current Ne than historical estimates and that L. cinereus may currently have a very large Ne. We found no genetic evidence of recent population declines and no evidence of population structure in either species. Genetic monitoring of migratory tree bats, specifically for the purpose of detecting population declines caused by wind turbine mortality, may be impractical due to the large effective population sizes and high levels of gene flow in these species. Future efforts should focus on developing genomic resources for these species, obtaining better estimates of mutation rates, and conducting range-wide population genetic studies in order to better estimate historical and current population sizes.