The intraspecific diversity of a species can give interesting insights into evolutionary mechanisms. This genotypic and phenotypic diversity allows species to adapt to different environments and to display favourable adaptive traits, which can lead to divergence between populations and with time, to the formation of lineages or even new species. Brown trout in Central Europe has split into five lineages (Salmo trutta species complex), mostly due to the allopatric separation of drainage systems. The Engadin, a region in the Swiss Alps, is part of the Danube drainage system and harbours brown trout populations with individuals from several lineages. The aim of my study was to assess the genotypic and phenotypic diversity of trout, and possible relationships between them. This was primarily done with trout from the Engadin but also by including populations from adjacent drainage systems. A genetic approach was used where I identified lineage-related mtDNA haplotypes and applied 13 microsatellite markers. Trout phenotypic data were obtained through measurements of skin colour, spot patterns and morphology. The results revealed that the Atlantic and Danube trout lineages in the Engadin still exhibit genetic differences, but also that these were admixed to a large extent. This suggests a scenario of extensive interbreeding between the lineages in this region. Additionally, I found that the variation in skin colour and spot patterns was enhanced in the Engadin compared to the other drainage systems. A correlation between genetic and phenotypic data was not evident. The large phenotypic variation in the Engadin could, at least in part, be the result of phenotypic plasticity altered by gene flow between phenotypically diverged lineages.