ABSTRACT We analyzed the bat assemblages found in protected areas in the state of Rio de Janeiro, Brazil, which is the best-sampled region of the Atlantic Forest. We selected 24 strict nature reserves and nine sustainable-use protected areas. We used data from inventories and complemented with data from the literature. We compared strict and sustainable-use protected areas, and tested whether the bat assemblages varied between habitat types. We tested the effect of geographic distance on the dissimilarity between bat assemblages, as well as the relationship between species composition and the size, mean altitude of the protected area, and capture effort. We compiled a total of 34,443 capture records, involving 67 species. Three species were captured only once, which raises cause for concern. Bat assemblages did not vary between protected area categories, but did vary among habitats with less than 1,000 captures. Assemblages were more similar to one another in geographically proximate areas. The size of the protected area and capture effort did not affect the composition of the bat assemblages, but altitude did influence this parameter. The Atlantic Forest is a priority biome for research and conservation, and reliable data on species distributions are essential for the development of conservation strategies.