Land-use change can have negative effects on threatened species by modifying their habitat and population dynamics. The habitat of the Endangered Patagonian cypress Fitzroya cupressoides (Mol.) Johnst. (Cupressaceae), a conifer endemic to the temperate forests of southern Chile and Argentina, has been transformed by land-use change and overexploitation. The impact of land-use change on the spatial pattern of F. cupressoides habitat from 1999 to 2011 was evaluated at the landscape level, using satellite images. Additionally, eight 20 × 25 m plots were established in four populations to assess their status. In each plot the density of F. cupressoides and the species richness of the associated plant communities were recorded and analysed, together with spatial patterns at the population and community levels. The loss of potential F. cupressoides habitat was 46% from 1999 to 2011 (38–100% for the four populations). The density of F. cupressoides was lowest in smaller habitat patches, where the number of plant species was higher and the matrix dominated by anthropogenic land-use. Land-use change was associated with a loss of potential habitat for F. cupressoides, and differences in the spatial patterns of habitat influenced the composition of remaining populations and communities. A landscape approach is recommended as a conservation planning strategy for F. cupressoides.