We evaluate the hypothesis of no geographic structure in the Huchen (Hucho hucho), a large, predatory salmonid endemic to the Danube basin. Forty-seven individuals sampled from throughout the Hauchen's native range were genetically characterized. Extremely limited sequence diversity across 1,800 bases of mtDNA (the complete control region and partial NADH-1 subunit) evidenced by four closely related mtDNA haplotypes was found. Nonetheless, the geographic distribution of mtDNA repeats (5-10, 82-bp long copies per individual) as well as allelic diversity across two microsatellite loci indicated large-scale geographic structure between the north-western (Austria and Slovenia) distribution area and eastern Slovakia nad Ukraine) or southern (Bosnia-Herzegovina and Montenegro) sample sites. An extremly slow rate of substitution for the H. hucho mtDNA is considered along with the alternative hypotheses to explain the limited mtDNA diversity. Considering the regional genetic structure implied by our data, we advocate restrictions on the transport of brood fish of yearlings across the range of the species distribution and sale of Huchen across international boundaries. Future genetic analysis to support local conservation and monitoring efforts must focus on developing a high-resolution screen that may be applied to identify hatchery versus naturally reproduction individuals in the wild.