Marine blue mussels (Mytilus spp.) are widespread species that exhibit an antitropical distribution with five species occurring in the Northern Hemisphere (M. trossulus, M. edulis, M. galloprovincialis, M. californianus and M. coruscus) and three in the Southern Hemisphere (M. galloprovincialis, M. chilensis and M. platensis). Species limits in this group remain controversial, in particular for those forms that live in South America. Here we investigated structural characteristics of marine mussels mitogenomes, based on published F mtDNA sequences of Northern Hemisphere species and two newly sequenced South American genomes, one from the Atlantic M. platensis and another from the Pacific M. chilensis. These mitogenomes exhibited similar architecture to those of other genomes of Mytilus, including the presence of the Atp8 gene, which is missing in most of the other bivalves. Our evolutionary analysis of mitochondrial genes indicates that purifying selection is the predominant force shaping the evolution of the coding genes. Results of our phylogenetic analyses supported the monophyly of Pteriomorphia and fully resolved the phylogenetic relationships among its five orders. Finally, the low genetic divergence of specimens assigned to M. chilensis and M. platensis suggests that these South American marine mussels represent conspecific variants rather than distinct species.