The sperm ultrastructure has been used to solve several systematic and phylogenetic problems in marine invertebrates. The sperm ultrastructure of the Chilean mussel Mytilus chilensis and Mytilus galloprovincialis corresponds to the ect-aquasperm type. Sperm from both taxa measured 55-60 µm between head (acrosome + nucleus), midpiece (only 5 mitochondria) and the flagellum which in its end piece has a smaller diameter tail. The differences between both taxa are clearly shown, in the structure of the acrosome and nucleus. Therefore, according to our results and those reported in the literature, we indicate that Chilean native mussel sperm is different from other species of the Mytilus complex (M. trossulus, M. galloprovincialis and M. edulis). These differences in sperm ultrastructure found in M. chilensis, are another trait that can be used to validate the taxonomic status of the species. Differences in sperm morphology are related with reproductive isolation, and probably will be useful to understand future data on speciation. Finally, we discussed the finding that Mytilus galloprovincialis sperm from Chile have an acrosome notoriously smaller than those reported for specimens from Europe and Africa, though they have a great similarity with specimens from Japan, as reported in the literature.