Allozyme analysis of 35 populations of the endemic New Zealand greenshell mussel Perna canaliculus (Gmelin 1791) indicated an absence of genetic structuring, whereas mitochondrial DNA (mtDNA) single-strand conformation polymorphism (SSCP) analysis of 22 of the same populations indicated a pronounced genetic discontinuity between northern and southern mussels at ~42°S latitude. The present study examines the genetic structuring of a subset of 19 New Zealand mussel populations using the randomly amplified polymorphic DNA (RAPD) technique. A genetic discontinuity was observed between northern and southern populations, which resulted from significant allele frequency differences, but no absolute differences between populations of these regions. Southern populations were genetically more diverse than northern populations, with the west coast of the South Island being the most distinct from northern populations. The RAPD data are consistent with the mtDNA data, indicating that both studies have resolved the population structure of P. canaliculus at a higher level than previous allozyme studies. The location of the genetic discontinuity coincides with major hydrographic features at ~42°S latitude. We hypothesise that restricted gene flow (larval transport), a consequence of present day coastal surface circulation patterns, influences the population genetic structuring of this species, an effect which is relatively recent in geological time (within the last 12000 yr).