Distribution modeling and vegetation suitability mapping were undertaken to assess (1) the role that past climate change played in fragmenting a subspecies of the endangered southern brown bandicootIsoodon obesulusand (2) the impacts of land cover change on the subspecies following European settlement of Australia. Based on a selection of bioclimatic variables, disjunctions in the broad distribution ofI. obesulus obesuluswere found. Vegetation maps representing the time of European settlement revealed two clear features. First, vegetation that was unsuitable for the subspecies corresponded to climatic disjunctions in its distribution, and, second, substantial additional areas were predicted to have suitable vegetation but not suitable climate. Vegetation mapping showed considerable change over two centuries after European settlement, so that most places that formerly had suitable climate and vegetation were cleared. Our analysis demonstrates that clearing of native vegetation has masked naturally occurring disjunctions in the distribution ofI. o. obesulus. This finding provides evidence that fragmented, regional-scale populations ofI. o. obesulusexisted prior to European settlement. Implications for conservation planning are discussed.