A unique community of four syntopic eagle species exists in north-central Kazakhstan. Questions about behaviour and genetics in these four species would benefit from the development of microsatellite markers. We isolated eight polymorphic microsatellite repeats (AAAG)n from the eastern imperial eagle (Aquila heliaca) genome using a hybridization enrichment technique. These loci revealed moderate diversity in a local population of eastern imperial eagles (observed heterozygosity 0.26–0.78), and were also polymorphic in steppe eagles (A. nipalensis) and white-tailed sea eagles (Haliaeetus albicilla). These primers may be polymorphic in other species of Aquila and Haliaeetus eagles.