• control region;
  • Danube;
  • introgression;
  • LDH-C1*;
  • microsatellites;
  • population genetics

Abstract  Stocking has had a considerable effect on wild brown trout, Salmo trutta L., populations throughout Europe. To elucidate this impact and to outline further management strategies, the genetic structure of 25 wild populations and five hatchery stocks from Czech Republic and Slovakia were analysed using mitochondrial (control region) and nuclear DNA (microsatellites, LDH-C1*) markers. Stocking practices have caused massive hybridisation between the Atlantic and Danube brown trout strains in the central Danube basin and have lead to a loss of among-population divergence in Slovakia and the eastern part of Czech Republic. Comparison with studies from neighbouring countries revealed substantial differences in haplotype, allele frequencies and genetic diversity across Central Europe. Differences in stocking management and origin of breeding stocks appear to be crucial factors for the spatial variability of the genetic structure of brown trout.