Abstract The abundance and distribution of large carnivores in Europe have been historically reduced. Their recovery requires multilevel coordination, especially regarding transboundary populations. Here, we apply nuclear and mitochondrial genetic markers to test for admixture level and its impact on population genetic structure of contemporary brown bears (Ursus arctos) from the Eastern, Southern, and Western Carpathians. Carpathian Mountains (Europe). Nearly 400 noninvasive brown bear DNA samples from the Western (Poland) and Eastern Carpathians (Bieszczady Mountains in Poland, Slovakia, Ukraine) were collected. Together with DNA isolates from Slovakia and Romania, they were analyzed using the set of eight microsatellite loci and two mtDNA regions (control region and cytochrome b). A set of 113 individuals with complete genotypes was used to investigate genetic differentiation across national boundaries, genetic structuring within and between populations, and movement between populations. Transboundary brown bear subpopulations (Slovakia and Poland) did not show significant internal genetic structure, and thus were treated as cohesive units. All brown bears from the Western Carpathians carried mitochondrial haplotypes from the Eastern lineage, while the Western lineage prevailed in the brown bears from the Bieszczady Mountains. Despite similar levels of microsatellite variability, we documented significant differentiation among the studied populations for nuclear markers and mtDNA. We also detected male‐biased and asymmetrical movement into the Bieszczady Mountains population from the Western Carpathians. Our findings suggest initial colonization of the Western Carpathians by brown bears possessing mtDNA from the Eastern lineage. Genetic structuring among populations at microsatellite loci could be a result of human‐mediated alterations. Detected asymmetric gene flow suggests ongoing expansion from more abundant populations into the Bieszczady Mountains and thus supports a metapopulation model. The knowledge concerning this complex pattern can be implemented in a joint Carpathian brown bear management plan that should allow population mixing by dispersing males.