The extent and intensity of European-induced changes to ecosystems in south-eastern Australia mean that remaining habitats, despite being degraded, are of high conservation value. Given the extinction of several species of native mammals in the last 160 years in the area, and conservation concerns regarding others, it is important to provide conservation managers with sufficient information to prevent further extinctions and maintain evolutionary potential of the species. A native, carnivorous marsupial, the Yellow-footed Antechinus (Antechinus flavipes) exists within these massively altered landscapes. We present conceptual models, derived from the literature, of persistence of populations of Yellow-footed Antechinus both before European colonization and in the 21st century. We conclude that preservation of large trees, restoration of fallen-timber volumes, spring flooding of floodplains and presence of vegetation corridors between forests should be undertaken to prevent local extinctions of Yellow-footed Antechinus. From historic and current gene flow, we identify remnant woodland and forest groupings that we consider should be managed as coherent units.