Context: Research on the impacts of anthropogenic habitat fragmentation has dominated landscape ecology for decades, yet our understanding of what drives species’ distributions in naturally fragmented landscapes remains limited. Objectives: We aimed to (i) determine whether rocky patches embedded within a ‘matrix’ of fire prone grasslands act as naturally fragmented landscapes for an endangered marsupial predator, the northern quoll (Dasyurus hallucatus), and (ii) reveal the extent to which within-patch, patch, landscape variables, and matrix condition drive the occurrence of northern quolls. Methods: We deployed remote sensing cameras for a total of 200 nights, at 230 sites spanning rocky and grassland habitats across 6000 km2 of the Pilbara bioregion of Western Australia. We examined the influence of within-patch, patch, landscape variables, and matrix condition on northern quolls using Generalised Linear Mixed Models. Results: We found strong evidence that northern quoll habitat is naturally fragmented, observing higher occurrence and abundance of quolls in rocky patches than the surrounding grassland matrix. Within rocky patches, quolls were more likely to use patches with higher vegetation cover and den availability (within-patch), lower amounts of edge habitat relative to patch area (patch), and larger amounts of surrounding rocky habitat (landscape). When quolls entered the matrix, they tended to remain in areas with high vegetation cover, close to rocky patches. Conclusions: Species occurrence in naturally fragmented landscapes is influenced by factors operating at multiple scales. Rocky habitats are naturally fragmented and vital to the conservation of a range of taxa around the world, including the northern quoll.