AbstractAimForest fragmentation is a major driver of biodiversity loss causing declines in species richness and functional diversity of biotic communities. Bats are essential components of ecosystems and are useful bio‐indicators of habitat disturbance, yet the response and vulnerability of bats to fragmentation have been poorly studied in Africa. We aim to assess the effects of forest biogeographical history and fragmentation on functional diversity of bats and their functional traits.LocationEastern Cape and southern KwaZulu‐Natal, South Africa.TaxonInsectivorous bats.MethodsWe surveyed forest‐utilizing bats to derive four functional diversity indices. Generalized linear models were used to assess the response of diversity indices to biogeographical history and fragmentation, represented by forest type and five landscape fragmentation metrics. RLQ and fourth‐corner analysis were used to investigate the interaction of traits with fragmentation metrics and forest type.ResultsPondoland Scarp forests displayed high functional richness, while Eastern Cape Dune forests exhibited high functional divergence yet low functional richness and dispersion. Two fragmentation metrics affected functional diversity dynamically: edge density had a positive effect on functional evenness; and dispersion was negatively affected by river length through forests. Results showed stronger interactions of functional traits with forest type than fragmentation metrics, with filtering effects on body size and wing morphology.Main conclusionsThe large‐scale processes related to biogeographical history, and associated forest structure, are important determinants of functional richness, divergence and dispersion of insectivorous bat communities. Scarp forests showed the highest species and functional richness as they experienced less extreme climatic extinction filtering than Mistbelt forests during the Last Glacial Maximum, whereas the low diversity of Eastern Cape Dune forests results from their younger evolutionary history and homogenous vegetation structure. Little is known of the sensitivity of bats to habitat fragmentation in Africa: here, we show larger‐sized insectivorous species; and species exhibiting low wing loading may be more vulnerable to fragmentation.