Knowledge of the conservation status of Bornean bats is biased towards areas considered to support high diversity in the northern Malaysian states. Few surveys have been undertaken in Indonesian Borneo, despite it representing over two thirds of the island's land area. We present the first description of a bat assemblage in Borneo's nutrient poor, or oligotrophic, forests (heath and peat swamp), habitats that have been considered depauperate in wildlife. We surveyed two protected areas in Central Kalimantan using harp traps supplemented by mist nets. We recorded 27 species, 18 of which were captured exclusively by harp traps. The bat assemblage of both sites was dominated by vespertilionids of the subfamily Kerivoulinae. The most abundant species, Kerivoula intermedia, accounted for 45% of standardized captures in Tanjung Puting National Park. At this site 15 species were represented by <10 captures each. Hipposideros ridleyi, Kerivoula lenis, Murina aenea and Murina rozendaali, four rare and threatened species, were recorded for the first time in Indonesia, and Phoniscus atrox, Murina cyclotis and Hipposideros doriae were recorded for the first time in Kalimantan. Estimation of species richness indicated that this inventory was almost complete for understorey, narrow-space, insectivores susceptible to capture in harp traps. It is likely that further surveys targeting open spaces, rivers, forest edges and the canopy will record species of other foraging guilds. The inventory exceeds those from other sites in Kalimantan because previous surveys have not used harp traps. However, it is a depauperate subset of assemblages studied in north Borneo, most likely because these sites are better known and are nearer to caves. Despite this relatively low diversity, our study shows that protected areas in oligotrophic forests provide valuable habitat for some of this island's rarest bat species, and are likely to become more important for bat conservation in light of widespread forest disturbance in Borneo.