The Pyrenean brown bear Ursus arctos population in the mountains between France and Spain is one of the smallest and most threatened populations of large carnivores in Europe. We assessed trends in brown bear habitat use in the Pyrenees and investigated the underlying environmental and anthropogenic drivers. Using detection/non-detection data collected during 2008–2014 through non-invasive methods, we developed dynamic occupancy models, accounting for local colonization and extinction processes. We found two non-connected core areas of occupancy, one in the west and the other in the centre of the Pyrenees, with a significant decrease in habitat use overall during 2008–2014. We also found a negative correlation between human density and bear occupancy, in agreement with previous studies on brown bear habitat suitability. Our results confirm the Critically Endangered status of the Pyrenean population of brown bears.