Mitochondrial DNA (mtDNA) restriction site polymorphism was examined in European populations of the mussels M. edulis, M. trossulus, and Atlantic and Mediterranean M. galloprovincialis. Haplotype frequency distributions and mtDNA phylogenetic relationships contradict earlier systematic hypotheses based on morphological and allozyme data. Hybridization and differential mtDNA introgression among Mytilus forms explain this lack of concordance, indicating that nuclear and mitochondrial DNA have evolved differently. Introgression of mtDNA haplotypes between Mytilus taxa varies geographically, and haplotype diversity decreases with latitude. It is proposed that Pleistocene events and current ecological factors influencing hybridization among geographically proximal taxa may explain these observations.