Some small European populations of the brown bear (Ursus arctos) are threatened by the risk of extinction in the near future. The reinforcement of these populations with bears from other regions might provide a solution to their future survival. However, before any population transfer, the different conservation units must be identified. The phylogeographic approach has been advocated for this purpose. The different European populations were assayed for mitochondrial (mt) DNA polymorphism. A remarkable degree of concordance was found between the geographic distribution and the mtDNA haplotypes. Two clearly distinct lineages differing by more than 7% in mtDNA control region sequences were found and, furthermore, the western lineage appears to be organized into two clades which correspond to two different ancestral refugia. The potential conservation units can be deduced from these results, and a management policy can consequently be inferred. This study clearly demonstrates the relevance of the molecular phylogeographic approach to the identification of conservation units.