Hybrid zones among mussel species have been extensively studied in the northern hemisphere. In South America, it has only recently become possible to study the natural hybrid zones, due to the clarification of the taxonomy of native mussels of the Mytilus genus. Analyzing 54 SNP markers, we show the genetic species composition and admixture in the hybrid zone between M. chilensis and M. platensis in the southern end of South America. Bayesian, non-Bayesian clustering and re-assignment algorithms showed that the natural hybrid zone between M. chilensis and M. platensis in the Strait of Magellan, Isla Grande de Tierra del Fuego, and the Falkland Islands shows complex architecture. It can be divided into three different areas: the first one is on the Atlantic coast where only pure M. platensis and hybrid were found. In the second one, inside the Strait of Magellan, pure individuals of both species and mussels with variable degrees of hybridization coexist. In the last area at the Strait in front of Punta Arenas City, fjords on the Isla Grande de Tierra del Fuego, and at the Beagle Channel, only M. chilensis and a low number of hybrids were found.  According to the proportion of hybrids, bays with protected conditions away from strong currents would give better conditions for hybridization. We do not find evidence of any other mussel species such as M. edulis, M. galloprovincialis, M. planulatus, or M. trossulus in the zone

Mussels (n = 160) from ten sampling sites in the Strait of Magellan, the Isla Grande de Tierra del Fuego, the Falkland Islands, and the Beagle Channel were collected between 2016 and 2018. The DNA was extracted from the mantle edge tissue by the phenol-chloroform method modified for mussels. All individuals were genotyped with a panel of 54 SNPs that have shown good genotyping performance and reproducibility using the Sequenom MassARRAY iPLEX genotyping platform. Individuals with a genotyping rate of less than 90% were excluded from further analysis.