This study investigated the vertical stratification of Old World fruit bats (Chiroptera: Pteropodidae) in relation to habitat structure and wing morphology, in a lowland Malaysian rain forest. In total, 352 fruit bats of eight species were captured within the subcanopy of the structurally complex old-growth forest during 72 306 m2 mist net hours of sampling. Fruit bat species that were grouped in relation to capture height were also grouped in relation to wing morphology – with those species predicted to have more manoeuvrable flight (i.e. lower wing-loadings and lower aspect-ratios) captured in increasingly cluttered airspaces. Thus, small differences in wing morphology are likely to be ecologically significant to the vertical stratification of bats. Hence, habitat heterogeneity may be a key factor promoting fruit bat species diversity in old-growth palaeotropical forests.