Human depopulation of rural mountain areas and the consequent abandonment of traditional land management are among the greatest driving forces behind changes in mountain ecosystems in Western Europe. Tree and shrub encroachment lead to an increase in landscape matrix uniformity and habitat fragmentation. For some animal species, this represents an unusual case of habitat loss caused by secondary succession. The animal species associated with this agro-pastoral habitat may suffer from decreased connectivity as a consequence. The Rock Partridge Alectoris graeca is a species endemic to European mountains that represents a model for investigating the impact of habitat loss. We compared the habitat suitability of the Apennine Rock Partridge prior to abandonment of traditional agro-pastoral activities by aerial photography with the current landscape, in order to investigate the effect of secondary succession on the distribution and viability of the species. We assessed the historical distribution (c. 1900–1950) by quantifying anecdotal evidence from interviews, and the current distribution (2005) from survey data. We applied ecological niche factor analysis and connectivity approaches to evaluate change in habitat suitability over this time scale. Moreover, to quantify landscape connectivity, we evaluated the relative importance of each patch in the two periods. Results indicated that to maintain a viable population in the Apennines, the species requires an ensemble of ecological conditions considerably different from the current situation. We observed a drastic decrease in connectivity as a result of a reduction in numbers and size of high suitability patches. This is most probably the primary cause of the current decline of the Rock Partridge population in the Apennines.