The aim of the present work is to increase the general knowledge about an economically important mussel species in Chile. Species of Mytilus are present in the southern cone of South America; however, there is still some controversy about species identification of samples from this area. The study herein presented attempts to: (1) corroborate the phylogenetic hypothesis defined for the Mytilus edulis species complex including taxa from a worldwide distribution; (2) evaluate the possible presence of the species Mytilus trossulus along the Chilean coast and determine if M. trossulus hybridizes with the local species; and (3) provide detailed data collected along the Chilean coast to help define the taxonomic status of Mytilus in South America. To this end, exhaustive sampling was conducted; Mytilus was collected from the Chilean coast and from the coasts of Argentina and Uruguay. Phylogenetic analysis and genetic divergence estimators were used to compare 426 Cytochrome oxidase I mitochondrial gene sequences and 190 16S RNA sequences of Mytilus species sampled from around the world. Following this, the time of divergence between northern hemisphere and southern hemisphere clades of Mytilus species was estimated. In addition, neither M. trossulus nor any associated hybrids were found along the Chilean coast. Finally, the identification of samples from the southern cone of South America is discussed including whether the samples should be identified as Mytilus planulatus or Mytilus platensis. In accordance with the taxonomic priority rules and the results presented here, the species identification frequently used in the literature for samples from the Chilean coast (Mytilus chilensis) may cease to be used.