Bats are important components in tropical mammal assemblages. Unravelling the mechanisms allowing multiple syntopic bat species to coexist can provide insights into community ecology. However, dietary information on component species of these assemblages is often difficult to obtain. Here we measured stable carbon and nitrogen isotopes in hair samples clipped from the backs of 94 specimens to indirectly examine whether trophic niche differentiation and microhabitat segregation explain the coexistence of 16 bat species at Ankarana, northern Madagascar. The assemblage ranged over 4.4‰ in δ15N and was structured into two trophic levels with phytophagous Pteropodidae as primary consumers (c. 3‰ enriched over plants) and different insectivorous bats as secondary consumers (c. 4‰ enriched over primary consumers). Bat species utilizing different microhabitats formed distinct isotopic clusters (metric analyses of δ13C–δ15N bi-plots), but taxa foraging in the same microhabitat did not show more pronounced trophic differentiation than those occupying different microhabitats. As revealed by multivariate analyses, no discernible feeding competition was found in the local assemblage amongst congeneric species as compared with non-congeners. In contrast to ecological niche theory, but in accordance with studies on New and Old World bat assemblages, competitive interactions appear to be relaxed at Ankarana and not a prevailing structuring force.