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Background  Large numbers of endemic species inhabit subantarctic continental coasts and islands that are characterised by highly variable environmental conditions. Southern hemisphere populations of taxa that are morphologically similar to northern counterparts have traditionally been considered to be extensions of such Northern hemisphere taxa, and may not exhibit differentiation amongst geographically isolated populations in the Southern Ocean. Smooth-shelled blue mussels of the genus  Mytilus  that exhibit an anti-tropical distribution are a model group to study phylogeography, speciation and hybridisation in the sea, and contribute to the theory and practice of marine biosecurity.    Methods  We used a single nucleotide polymorphism (SNPs) panel that has the ability to accurately identify reference Northern and Southern hemisphere  Mytilus  taxa to test for evolutionary differentiation amongst native Southern Ocean island populations.    Results  Native mussels from the Falkland Islands and the Kerguelen Islands exhibited greatest affinity to native  M. platensis  d’Orbigny 1846 from the Atlantic coast of South America. The major Southern Ocean current flow from west to east is likely to explain the spreading of  M. platensis  to remote offshore islands, as adults via the process of rafting or perhaps directly as larvae. SNPs variation revealed that mussels from Tasmania were native and clearly differentiated from all other blue mussel groups in the Southern and Northern hemispheres. The native mussels  M. planulatus  from Tasmania and from mainland New Zealand (NZ), and tentatively  M. aoteanus  from the two NZ Southern Ocean offshore island groups (the Auckland Islands and Campbell Island), formed a distinct  M. galloprovincialis –like Southern hemisphere group with closest affinity to Northern hemisphere  M. galloprovincialis  from the Mediterranean Sea. In all cases, the SNPs revealed evidence of hybridisation between two or more distinct taxa. The invasive Northern hemisphere  M. galloprovincialis  was identified only in Tasmania, amongst native mussels of a distinct Australian  M. planulatus  lineage.    Conclusion  Overall, our results reveal that Southern hemisphere island mussels have mixed genome ancestry and are native, not introduced by human activities. The preservation of distinct evolutionary lineages of Southern hemisphere species needs to be an ongoing focus of conservation efforts, given that population sizes on some of the remote offshore oceanic islands will be small and may be more easily adversely affected by invasion and subsequent hybridisation and introgression than larger populations elsewhere.    Electronic supplementary material  The online version of this article (10.1186/s12983-019-0332-y) contains supplementary material, which is available to authorized users.

Cryptic diversity in smooth-shelled mussels on Southern Ocean islands: connectivity, hybridisation and a marine invasion