Bonelli's eagle Hieraaetus fasciatus is a threatened cliff-nesting raptor mainly distributed in the coastal regions of the Mediterranean. The European population has declined and the species is considered Vulnerable in Spain. Before effective conservation programmes can be proposed the causes of this decline need to be considered. In a monitoring programme of the population of Bonelli's eagle in Murcia carried out since 1983 we observed a marked decline, followed by a period of stability that began in 1990. Using demographic data (territorial bird survival, non-territorial bird survival, and fecundity) for 1990–1998 we applied a territorial occupancy model to evaluate management alternatives for the species. The model, which assumes demographic stability, estimates an equilibrium proportion of habitat occupancy as a function of life history parameters, dispersal behaviour and habitat suitability. In spite of some limitations the model identified the most important conservation measures required for an increase in the proportion of territories occupied: the improvement of the survival of both territorial and non-territorial birds, and an increase in the proportion of suitable habitat.