Major threats to the Vulnerable greater spotted eagle Aquila clanga are habitat loss and hybridization with the lesser spotted eagle Aquila pomarina, but no quantitative studies have been carried out to understand these processes. In Estonia the known remaining A. clanga population comprises only five pure and nine mixed pairs. We describe their habitat at the scale of both the home range and nest site, and use logistic regression models for comparisons with random forest plots and nest sites of A. pomarina. The territories of A. clanga were characteristically near waterbodies, where the species' nesting preference was for dense forest with a pronounced old-growth structure. Habitats of the two species were distinct at both spatial scales. Open natural landscapes were favoured by A. clanga but avoided by A. pomarina. Within its home range A. clanga occupied old wet stands containing black alder, birch and pine, whereas A. pomarina preferred old spruce stands. Multivariate models, which summarized these differences between the two species, did not reveal distinct habitat features of mixed pairs compared with A. clanga pairs. Hence, interbreeding pairs may occupy previous A. clanga territories, and these deserve similar protection to those currently inhabited by A. clanga pairs.