Wetlands in the Biebrza Valley, north-east Poland, are inhabited by two closely related Aquila species: the more numerous Lesser Spotted Eagle A. pomarina prefers human-transformed landscapes, whereas the very rare Greater Spotted Eagle A. clanga is associated with natural marshy landscapes. At least since the last decade of the 20th century, these two species have been known to hybridise in the broad zone of their sympatric occurrence in Europe. The aim of the present study was to compare habitat preferences of both spotted eagle species in order to detect which environmental factors could increase the probability of hybridisation. We analysed nesting and hunting habitats for 148 breeding territories (61 of A. pomarina, 56 of A. clanga and 31 of mixed pairs). As expected, the presence of breeding Greater Spotted Eagles was associated with non-transformed marshy landscapes, whereas Lesser Spotted Eagles clearly preferred human-transformed areas. We hypothesised that mixed pairs should occur in intermediate habitat, confirming this assumption by analysing several variables: distance to human settlements, distance to open areas, and proportion of wetlands, shrublands, grasslands, agricultural mosaic and arable land. Results of this study suggest that some landscape changes can enable two species with different habitat requirements to inhabit the same area and hybridise. This scenario has potential conservation implications for the rarer species, Greater Spotted Eagle, which has narrower habitat preferences.