Conservation genetics study of huchen in Slovenia recommends river system‐based management and indicates self‐sustainability of the middle Sava population.

The middle part of the Sava River in Slovenia provides one of the longest free‐flowing habitats for huchen, a threatened species that is also protected by the European Habitats Directive. However, there are plans for the construction of a chain of hydropower plants along this stretch of river. It has previously been assumed that huchen is no longer self‐sustainable here, but dependent upon stocking with hatchery‐reared fish.Using microsatellite and mitochondrial DNA, the genetic structure of huchen in its entire range in Slovenia was analysed with the particular aim of assessing the self‐sustainability of the species in the middle Sava.Using factorial correspondence analysis and assignment tests, a distinct genetic cluster was identified for each of the three main river systems in the country (Sava, Kolpa and Mura–Drava). In the middle Sava, a genetic admixture between stocked and local individuals, observed beyond F1, and a unique genetic substructure not corresponding to the stocking sources, were found.These results indicate the self‐sustainability of the middle Sava population and justify its protection. The estimated effective population size in the middle Sava is below the accepted minimum, and additional fragmentation arising from dam construction would cause the genetic breakdown of this huchen population.To preserve local genetic pools and possible inter‐population adaptive differentiation, we recommend that the three, historically isolated, river system‐bound populations (from the Sava, Kolpa and Mura–Drava) are managed separately. However, separate management of the small, isolated populations in the once free‐flowing Sava river system is not encouraged as it may cause their genetic impoverishment.The potential impact of this study on the conservation management of huchen more widely is discussed, with emphasis on the Balkans, where large populations still exist and their management is just beginning. [ABSTRACT FROM AUTHOR]