The need to understand how anthropogenic landscape alteration affects fauna populations has never been more pressing. The importance of developing an understanding of the processes behind local extinction is widely acknowledged, but inference from spatial patterns of fauna distribution continues to dominate. However, this approach is limited in its ability to generate strong predictions about future distributions and local extinctions, especially when population-level responses to landscape alteration are subject to long time lags. We review the potential for indices of physiological stress and condition to contribute to understanding of how landscape pattern affects species persistence. Such measures can indicate habitat quality from the perspective of the individual animal, and can reveal environmental stressors before their negative consequences begin to manifest at a population level. Spatial patterns of chronic stress may therefore yield valuable insight into how landscape alteration influences species. We propose that the emerging disciplines of conservation physiology and macrophysiology have much to offer spatial ecology, and have great potential to reveal the physiological pathways through which habitat alteration affects fauna populations and their persistence in fragmented landscapes.