Human modification of landscapes typically results in many species being confined to small, isolated and degraded habitat fragments. While fragment size and isolation underpin many studies of modified landscapes, vegetation characteristics are less frequently incorporated. The relative influence of biogeographic (e.g. size, isolation) and vegetation parameters on assemblages is poorly understood, but critical for conservation management. In this study, a multiple hypothesis testing framework was used to determine the relative importance of biogeographic and vegetation parameters in explaining the occurrence of an assemblage of small mammals in 48 forest fragments in an agricultural landscape in south-eastern Australia. Fragment size and vegetation characteristics were consistently important predictors of occurrence across species. In contrast, fragment isolation was important for just one native species. Differing abilities of species to move through the landscape provide a reasonable explanation for these results. We conclude that for effective conservation of assemblages, it is important to: (1) consider differing responses of species to landscape change, and (2) move beyond a focus primarily on spatial attributes (size, isolation) to recognise that landscape change also has profound effects on habitat composition and quality.