Globally, species with small distributions face disproportionate extinction risk, with the impacts of land use change more likely to have catastrophic consequences. Identifying, protecting and managing sites where such species occur is essential for minimising their extinction risk. Yet across Australia, efforts to protect and manage such species' habitats have hitherto been insufficient. Here, we present an example of an analytical and interpretive pathway for the conservation of such species, for a continental-scale case study. We identified 305 Critically Endangered species that have narrow ranges (<20,000 km²), and are distributed in fewer than six discrete patches. We refined existing species' habitat maps with advice from 18 experts via a modified Delphi approach. We assessed how much of each species' habitat is outside protected areas and considered to have agricultural capability, potentially elevating risk of conversion. We identified ∼85,000 km² of habitat (∼1% of Australia) for these 305 species that must receive protection and management if the nation is going to meet its commitment to halt new extinctions. Approximately half of this habitat is outside the protected area estate, including the entire distribution of 39 species. Approximately 55% of habitat outside of protected areas had at least some agricultural capability. Protecting and managing the habitats of these narrow-range species should be a high priority in state and national conservation policy. Our case study serves as a template for the identification of important habitat for threatened species and could be applied in other regions of the world.