Understanding the evolutionary and ecological processes that have shaped current patterns of biodiversity is crucial in the planning and implementation of broad scale conservation management. The temporal and spatial pattern of diversity across a landscape can help identify areas that have acted as climatically stable refugia historically, or do so currently. This has important implications for conservation efforts that try to maximise the evolutionary potential of species, as well as maintaining existing biodiversity. Northern Australia has recently reported catastrophic species decline, particularly in mammals, due to a series of threats. Here we apply an integrative approach utilising molecular analyses and spatial modelling to determine whether disjunct populations of a potentially rare, endemic mammal, the scaly-tailed possum (Wyulda squamicaudata) exhibit differentiation associated with biogeographic barriers or a recent decline. Significant but low genetic differentiation between the east and west Kimberley populations was detected. Principal component analyses indicate potential climatic niche differences that could support recent localised adaptations. Climatic reconstructions back to the last glacial maximum (LGM) indicate areas of suitable habitat have substantially shifted through time for W. squamicaudata and suggest multiple areas of refugia across the Kimberley since the LGM. Further comparative research is required to establish a biogeographical framework that will assist in our understanding of processes that have shaped biodiversity in northern Australia and assist in conservation planning.