In the Doubs River (Rhone drainage) two distinct brown trout (S. trutta) phenotypes are observed. One phenotype is locally called Doubs trout and is characterized by four black stripes on the sides, similar to perch (Perca fluviatilis L.) and the other is the common phenotype of the fluviatile ecotype of brown trout, Salmo trutta f. fario. Protein data for three samples from the Doubs show that the Doubs trout belongs to the Mediterranean population group of brown trout, whereas the fario phenotype originates from stocking with hatchery strains of Atlantic basin origin. The two forms, however, do not hybridize freely. This is indicated by considerable gametic phase disequilibrium between alleles of hatchery and Doubs trout at one sampling site, and by lack of intermediate genotypes and phenotypes at another sampling site. The introgression patterns observed at the two sites suggest that differences in local habitat conditions can affect the degree of hybridization and introgression.