The distribution of the Ural Owl (Strix uralensis) in Europe shrank dramatically at the end of the nineteenth century, largely through direct persecution. No genetic information on this species is available that could provide a basis for ongoing conservation and breeding programs. Here, we genetically analyzed wild and captive populations of European Ural Owls to provide data that can be used to establish sound and sustainable management strategies. We analyzed mitochondrial and nuclear markers to evaluate the morphology-based concept of two subspecies (Strix uralensis liturata and Strix uralensis macroura), to gain insights into the phylogeographic population structure, and to determine genetic clusters for management implications. Our results supported neither the morphological subspecies concept nor a strong phylogeographic population structure. However, they pointed toward a noteworthy genetic exchange in the western range of the distribution of this species. Structure analysis revealed five genetic clusters. We propose that genetic-cluster-based management is better suited to the conservation of European Ural Owls than the separate consideration of each local population. If applied in supportive breeding programs, genetic cluster recognition and its contribution to divergence and diversity would help to preserve the genetic variability of the captive breeding population and enable optimal genetic tuning of the captive population to correspond to the genetic constitution of the supported population.