Since European occupation of Australia, human activities have caused the dramatic decline and sometimes extinction of many of the continent’s unique species. Here we provide a comprehensive review of threats to species listed as threatened under Australia’s Environment Protection and Biodiversity Conservation Act 1999. Following accepted global categories of threat, we find that invasive species affect the largest number of listed species (1257 species, or 82% of all threatened species); ecosystem modifications (e.g. fire) (74% of listed species) and agricultural activity (57%) are also important. The ranking of threats was largely consistent across taxonomic groups and the degree of species’ endangerment. These results were significantly different (P < 0.01) from recent analyses of threats to threatened species globally, which highlighted overexploitation, agriculture and urban development as major causes of decline. Australia is distinct not only in the biodiversity it contains but also in the extent and mixture of processes that threaten the survival of these species. Notably, the IUCN threat classification scheme separates the numerous threats (e.g. urban development, agriculture, mining) that cause habitat loss, fragmentation and degradation, hence further research is required to quantify the net impact of these types of habitat change. We provide feasible suggestions for a more coordinated national approach to threatened species conservation, which could provide decision makers and managers at all levels with improved resources and information on threats and management. Adequate policy, legislative support and funding are critical for ensuring that on-ground management is successful in halting the decline of Australia’s threatened species.