ABSTRACT: Polymorphic microsatellite markers were employed to assay genetic variation in 14 populations of the endemic New Zealand greenshell mussel Perna canaliculus, which is continuously distributed across ~11.5° of latitude. Previous population genetics assessments of this species have identified a pronounced and ~1.3 million year old genetic discontinuity at ~42°S, just south of Cook Strait, the major break between the North and South islands. In addition to this genetic structuring, the present seascape genetics analysis of 7 environmental and 3 geospatial variables revealed that sea surface temperature (SST) explains far more genetic variation (among populations and individuals) than any other variable. Genetic variation across the full distributional range of P. canaliculus is, therefore, best explained by SST, which suggests that a contemporary temperature-related selective force is acting on greenshell mussels from the subtropical north to the cold temperate south. The identification of this association between environmental and genetic variation highlights how previously unrecognised patterns of genetic structure may be revealed by the examination of environmental variation and provides important leads for new research directions.