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Genetic structure of the Imperial Eagle ( Aquila heliaca ) population in Slovakia The distribution of the Imperial Eagle ( Aquila heliaca ) in the Carpathian Basin is not continuous, since western and eastern breeding pairs are separated by 150 km from each other in Slovakia, and 70 km in Hungary. In the present study our aim was to examine whether this geographical distance has resulted in any genetic separation between the Western and Eastern Slovak breeding groups. We have used 132 shed feathers and 128 blood samples collected in the fields geographically representing the whole of the Slovak breeding population, and included all juveniles ringed between 2004 and 2006. After successful DNA extractions we have determined the sex, microsatellite DNA-profiles and mtDNA control region haplotypes of the specimens. Data were integrated in a common Hungarian-Slovak "DNA-fingerprint" database, making identification of the same specimen possible when recaptured. Based on a subsample of the collected individuals, the genetic structure of the Slovak population was tested using ten microsatellite loci and mtDNA control region haplotypes, and marginally significant genetic differentiation was found between western and eastern subpopulations. These results suggest that, in spite of the large dispersal capacity of the species, a relatively small geographic distance can also decrease the exchange rate of individuals between subpopulations. As this result involves only samples from the northern part of the breeding area, major conclusions concerning genetic structure and gene flow of Imperial Eagles in the entire Carpathian Basin population cannot be drawn without sampling and analysing the southern subpopulations in Hungary.