Southeast Asia is home to over 25 % of the world's bat fauna, but rapid rates of deforestation and habitat degradation threaten species across the region. Ecological bat research in Southeast Asia, which has hitherto lagged far behind that of Neotropical countries, is now gaining momentum with burgeoning efforts to assess the response of bat diversity to anthropogenic habitat modification. Central to interpretation of diversity patterns in disturbed landscapes is an understanding of assemblage composition and dynamics in relatively unmodified habitats. Fifteen years of research in a Malaysian primary rainforest has provided some understanding of bat assemblage structure and spatiotemporal variability in old-growth forests and has generated predictions of ensemble vulnerability that have largely been supported by empirical studies in the surrounding fragmented landscape and other parts of Southeast Asia. The forest-interior insectivorous ensemble, members of the Rhinolophidae, Hipposideridae, Kerivoulinae, and Murininae, is particularly vulnerable to forest loss and degradation, and this group can be further subdivided by their roosting ecology. By virtue of their greater vagility, cave-roosting forest-interior species are somewhat more resilient to fragmentation and degradation than species that depend on forest structures for roosts (cavities, foliage). However, as disturbance intensifies, cave-roosting species are also lost from assemblages and are further imperiled by cave disturbance. I advocate that future research focuses on testing the generality of the findings and predictions from the Malaysian landscape in other parts of Southeast Asia and on determining differential vulnerability within the other Southeast Asian bat ensembles.