The dataset contains records of a key prey species of Bonelli’s Eagle (Aquila fasciata) and other large birds of prey, the Rabbit (Oryctolagus cuniculus) (Mammalia, Lagomorpha), collected in the lower valley of River Sabor (NE Portugal), in the scope of the long-term Ecological Monitoring Program (PME) of the Baixo Sabor Hydroelectric Dams (AHBS), promoted by EDP – Energias de Portugal, S.A. This dataset includes results of line transects performed each season (winter, spring, summer and autumn), in the known territories of the Bonelli's Eagle in the lower Sabor river valley, from February 2010 to September 2014. Data consists of presence signs (scats, latrines) recorded per transect surveyed.