Knowledge of the distribution and natural history of bats in Southeast Alaska is limited. We conducted capture and acoustic surveys for bats throughout Southeast Alaska in 2005 and continued surveys on Prince of Wales Island in 2006. We documented capture success, relative abundance, morphology, and periods of reproduction for each species. Capture success varied by species, location, and type of capture site. Little brown myotis (Myotis lucifugus; Le Conte 1831) were captured most frequently, followed by California myotis (M. californicus; Audubon and Bachman 1842), Keen's myotis (M. Keenii; Merriam 1895), and long-legged myotis (M. volans; Allen 1866). We captured little brown myotis throughout the region, Keen's and California myotis as far north as Juneau, and long-legged myotis in the southern part of the region. Silver-haired bats (Lasionycteris noctivagans; Le Conte 1831) were not captured, but were sighted on Prince of Wales Island and acoustic data indicate they may occur as far north as Juneau. Based on low rates of detection, all species appear to occur in low densities in Southeast Alaska. Better understanding of population status and trends, habitat ecology, and response to forest management is needed to identify essential habitat elements and prioritize conservation strategies in this region.