Genomic evidence has confirmed that the native Chilean blue mussel is genetically distinct from the Northern Hemisphere M. edulis, M. galloprovincialis and M. trossulus[4] and also genetically different from Mytilus platensis,[5] the other species of smooth shelled mussel from South America.

Modern genetic studies based on single-nucleotide polymorphism (SNP) have demonstrated that the Chilean mussel is genetically different of both the Mediterranean mussel (Mytilus galloprovincialis) and the North Atlantic Mytilus edulis.

Evidence collected until 2021 recognized several blue mussel species in South America, including native M. platensis, introduced M. galloprovincialis from the Mediterranean, and possibly-introduced M.

[12][13] Using nuclear DNA markers, Borsa et al. (2012) confirmed earlier results from allozymes[14] that most populations in the south of the South American continent indeed represent a native Southern Hemisphere lineage of the blue mussel, for which they suggested to use the subspecies name Mytilus edulis platensis[12] (now M. platensis).

The same authors questioned the earlier identifications of the Montevideo mussel in Southern Chile as "M. galloprovincialis"[3] because the genetic markers then used could not help distinguishing M. galloprovincialis from any of the two native blue mussel species from the Southern Hemisphere,[12] now referred to as M. planulatus and M. platensis.