The Chilean blue mussel formerly Mytilus chilensis Hupe 1854, have been recently subject to a taxonomic revision using electrophoretically generated genetic data concluding that mussels from South America should be included tentatively in Mytilus edulis. The molecular genetic characterization (restriction fragment length polymorphism) of samples from 8 natural populations along the whole natural distribution of the Chilean blue mussel using 3 PCR-based nuclear DNA markers (ITS, Glu-5 and Me) was carried out. One of the markers (ITS) showed a similar banding pattern than M. edulis and M. galloprovincialis, whereas the other markers (Glu-5 and Me) showed a specific banding pattern found only in M. galloprovincialis. Also, a very low number (3.9%) of mussel hybrids (M. edulis–M. galloprovincialis) using two codominant markers was detected in the present study. The molecular evidence suggests that M. galloprovincialis is present in the southern coast of Chile, whereas no evidence for the occurrence of Mytilus trossulus was found.