The Golden Eagle (Aquila chrysaetos) is widely distributed in the northern Hemisphere and is thus an ideal candidate to explore large-scale biogeographic patterns. In recent years, Golden Eagle population genetics has gained considerable attention. However, the Eastern Palearctic region, a numerical stronghold for the species, is one of the least genetically studied regions within its geographic range. In West Mongolia, the Altai (Altay) Kazakhs collect wild Golden Eagle nestlings from eyries or trap juveniles and subadults on passage during seasonal movement and migration for traditional hunting, providing easy access for researchers to sample falconry eagles for population genetic analyses. We analyzed a 402-bp fragment of the mitochondrial control region and 14 nuclear microsatellite loci in combination with previously published genetic data to assess phylogeographic patterns, levels of genetic diversity, and fine-scale structuring of the Golden Eagle population within the Mongol-Altai Mountains. Golden Eagles in the Mongol-Altai Mountains exhibited overall high levels of genetic diversity. Mitochondrial DNA data across the species' geographic range reveal various stages of differentiation within the Holarctic clade: whereas divergence between the Western and Eastern Palearctic is relatively shallow, the Eastern Palearctic and Nearctic show a deeper divergence, although these geographic regions have not yet reached reciprocal monophyly. These patterns might reflect past climatic oscillations: Northern Europe may have been recolonized by Golden Eagles from the Eastern Palearctic region, and continental populations might still be connected by long-distance dispersers, but the Eastern Palearctic and Nearctic were likely connected via Beringia during the Quaternary and are today largely isolated from each other.

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