The size and spatial arrangement of habitat patches are important predictors of the persistence of threatened species living in fragmented habitats. If conservation biology succeeds to accurately quantify these predictors, we can use them to identify priority areas for conservation. To study the large-scale relationship between the distribution of distinct habitat patches and the occurrence of the threatened Western Capercaillie Tetrao urogallus, we developed a patch occupancy model for the species in the Swiss Alps. Thereto, we first confirmed the existence of a local population for 55 % of the patches in the field. Logistic regression was then used to predict patch occupancy as a function of patch area, isolation, connectivity, relative altitude and biogeographic region. The probability of a patch being occupied increased with patch size and increasing altitude, and decreased with increasing distance to the next occupied patch. A sensitivity analysis revealed that patch size and isolation were the most and second most important predictors of the model, respectively. The model is a useful tool to designate priority areas, additional smaller patches with a high probability of being inhabited and stepping stones within a regional network designed to conserve Capercaillie in a landscape with fragmented habitat.