Understanding how native mammals have responded to ecosystem modification since European settlement is critical for their conservation management. Unfortunately, historical data is limited, and our ecological understanding is instead heavily biased towards modern studies, mostly post-1960s. Consequently, critically important information about past conditions and ecological changes is often surmised, with modern conditions and ecological patterns perceived as close to natural or normal. Recently obtained information from subfossil deposits in south-eastern Australia indicates that mammal declines have been recent, rapid and underestimated, and that many assumptions about species’ ecology, biogeography, status and overall ecosystem health require re-evaluating. Of particular note, many species now rare and geographically restricted recently occupied a greater range of habitats, often at high abundances. Many species are experiencing niche-denial, whereby they are being excluded from their original niche, and cannot function as they did historically, which has wide-scale consequences for ecosystem function and management. The pattern of decline indicates that predation by exotic predators is the principal causal factor, especially when greatest declines have occurred to terrestrial species in structurally open habitat types, including forested habitats that have experienced limited disturbances by factors considered responsible for declines in other regions of Australia. Researchers must recognise that ecosystems have been highly modified and that species are potentially constrained from carrying out their ecological functions, and therefore need to exercise caution when making broad generalisations from their studies.