In the 1990s, the Pilliga forests were carrying the largest population of koalas west of the Great Dividing Range in New South Wales (NSW). Whereas the NSW koala population in its entirety was thought to be in decline, the Pilliga population stood out as potentially increasing. By 2007, anecdotal evidence suggested that the population was in decline. We undertook surveys of koalas in the Pilliga forests that repeated surveys undertaken between 1991 and 2011. We found that koalas had declined and were found in only 21% of sites in which they were observed in the initial surveys-by any measure, a 5-fold drop in occupancy in less than two decades is severe. Declines occurred evenly across the Pilliga, with persistence at a site seemingly related to a high initial density of koalas rather than to a slower rate of decline. Sites where koalas persisted were characterised as having higher temperatures and lower rainfall relative to other sites, being close to drainage lines with deeper soils and having a lower occurrence of fire. This pattern fits with the observation in the recent surveys that koalas were next to drainage lines in the western half of the Pilliga and fits with the suggestion that koalas show refugial persistence. Recovery from this point is not assured and will depend on how we manage the landscape, particularly with the threat of climate change. This will likely require active management within an adaptive management framework, such as restoration of refuges, and not simply habitat reservation.