PCR amplification and direct sequencing of regions of the cytochrome b and 16S rRNA mitochondrial genes was carried out on Italian and Irish populations of the brown trout (Salmo trutta) species complex. These included S. t. marmoratus, S. t. macrostigma, Salmo carpio, and Salmo fibreni collected in Italy, and S. t. trutta morpha fario, from both Italy and Ireland. Samples of Atlantic salmon (Salmo salar) were also examined and used as an outgroup in the phylogenetic analysis. Results based on 592 bp indicated differentiation between fario morphs from Italy and Ireland. Despite the large phenotypic differences within Italian salmonids, very low genetic variation was found. On the basis of the mtDNA sequences studied, S. carpio and S. fibreni, which have been described as good species, are genetically undifferentiated from the other Italian taxa. The finding of a haplotype from Ireland in the Brenta River in Italy stresses the importance of conservation genetics studies aimed at identifying and preserving native genotypes.