1. The present study was designed to characterize the genetic structure of brown trout (Salmo trutta) populations from the southern Balkans and to assess the spread of non-native strains and their introgression into native trout gene pools. We analysed polymorphism at nine microsatellite loci in seven supposedly non-admixed and three stocked brown trout populations.
2. The analyses confirmed the absence of immigration and extraordinarily strong genetic differentiation among the seven non-introgressed populations in parallel with low levels of intrapopulation genetic variability. In contrast, analyses of the stocked populations revealed that the genetic integrity of the local populations had been substantially changed, and the populations must be characterized as hybrid swarms. The pattern of population differentiation observed at microsatellites contrasted to that depicted previously by mtDNA variation. However, the close relationships between populations from the Danube and Axios river systems proposed solely by microsatellites could be explained by palaeogeographic events.
3. Our research showed that most of the populations examined represent unique gene pools, whose existence is critically compromised. Therefore, appropriate management and conservation strategies should be developed urgently in order to protect the subspecific biodiversity and to reverse currently negative trends.