We studied a sympatric and crossbreeding population of the Lesser and the Greater Spotted Eagle in the Biebrza Valley, NE Poland. In order to follow the dynamics of hybridisation and its possible causes we monitored these two species between 1996 and 2012, using visual and genetic species identification. Individuals in up to 51 territories annually were determined as one of the two species or as a hybrid according to plumage characteristics. Feathers from adults and chicks from 114 broods were collected and genotyped using 30 nuclear markers. Hybridisation was observed with both methods already at the beginning of the study, and showed a significantly increasing trend. The proportion of broods producing hybrids of the Greater and the Lesser Spotted Eagle increased during the study by over 30%. The percentage of territories occupied by pure Greater Spotted Eagle pairs declined to 50% at the end of the study. The increasing number of mixed pairs highly significantly correlated with the decreasing number of pairs of the rare Greater Spotted Eagle, but weakly with the numbers of the more common Lesser Spotted Eagle. Mate replacement was frequently recorded and favoured the Lesser Spotted Eagle or hybrids. Adult males were the most often replaced sex (71%), possibly due to their higher mortality. Sex ratio at the nestling stage did not diverge from 1:1. Overall, 13 cases of within-pair species composition change were recorded, leading mostly to hybridisation (61%), but sometimes also to re-establishment of pure A. clanga pairs (23%). Alteration of habitat towards that preferred by the Lesser Spotted Eagle and differential sex-mortality are discussed as the most possible causes of the increasing crossbreeding rate.