European-settlement-related impacts over the past 200 years pose many challenges for the conservation and restoration of Australia's ecosystems. Landscape modification, associated habitat loss and the introduction of exotic species have caused the extinction and mainland extirpation of numerous vertebrates. This process happened so quickly that many species became locally or functionally extinct before their presence was documented. A growing body of research on Holocene fossil accumulations is providing insights into the composition and biogeography of Australian ecosystems prior to European settlement. This review explores the similarities between palaeo- and neo-ecology and how Holocene (last 10,000 years) assemblages can be used by neo-ecologists, conservation managers and policy makers to identify and fill gaps in knowledge and contribute to the management and restoration of Australia's degraded ecosystems.