Determining the causes of mortality in endangered species is essential to understanding the possible reasons behind their decline and to facilitating the implementation of mitigating steps. The southern bent-winged bat (Miniopterus orianae bassanii) is a critically endangered Australian bat whose population numbers have decreased over the past 50 years. As part of a larger investigation to determine if disease could be a contributing factor to the decline, 27 southern bent-winged bats and one closely related eastern bent-winged bat (Miniopterus orianae oceanensis) that died during the study were necropsied and examined histologically. Trauma was the most common cause of death in the southern bent-winged bats, which mostly occurred at one site where fencing and other infrastructure was positioned around a key breeding cave. In response to these findings, management actions have been implemented to reduce this infrastructure-associated mortality of southern bent-winged bats. The single eastern bent-winged bat examined had a severe dermatitis caused by the mite Notoedres muris.