A major conclusion of studying metapopulation biology is that species conservation should favor regional rather than local population persistence. Regional persistence is tightly linked to size, spatial configuration and quality of habitat patches. Hence it is important for the management of endangered species that priority patches can be identified. We developed a predictive model of patch occupancy by capercaillie, a threatened grouse species, based on a single snapshot of data. We used logistic regression to predict patch occupancy as a function of patch size, isolation, connectivity, relative altitude, and biogeographical area. The probability of a patch being occupied increased with patch size and increasing altitude, and decreased with increasing distance to the next occupied patch. Patch size was the most important predictor although occupied patches varied considerably in size. Our model only uses data on the number, size and spatial configuration of habitat patches. It is a useful tool to designate priority areas for conservation, i.e. large core patches with high resilience in habitat quality, smaller island-patches that still have high probability of being inhabited or becoming recolonised, and patches functioning as “stepping stones”. If capercaillie is to be preserved, habitat suitability needs to be maintained in a functional network of patches that account for size and inter-patch distance thresholds as found in this study. We suggest that similar area-isolation relationships are valid for almost any region within the distribution range of capercaillie. The thresholds for occupancy are however likely to depend on characteristics of the respective landscape. The outcome of our study emphasises the need for future investigations that explore the relationship between patch occupancy, matrix quality and its resistance to dispersing individuals.