We investigated population genetic structure within and between ocean basins in the common mesopelagic copepod, Haloptilus longicornis, using the mitochondrial marker cytochrome oxidase subunit II (mtCOII, 43 locations, n 5 1059). We found highly significant genetic divergence among ocean basins (global F ST 5 0.20; p , 0.00001), with the exception of relatively weak genetic divergence between the South Atlantic and Indian oceans. Strong genetic breaks also were observed between populations in the northern and southern subtropical gyres of both the Atlantic and Pacific oceans (Atlantic: F CT 5 0.21, Pacific: F CT 5 0.15, AMOVA, p , 0.00001 for both oceans; where F CT measures genetic divergence among groups). In the Atlantic, a region of low abundance for H. longicornis in equatorial waters coincided with the location of the observed genetic break (, 0-12uN), suggesting the presence of a physical or bio-physical barrier that effectively limits migration among subtropical gyre systems for this species. Using oceanographic data from a basin-scale transect, we provide the first environmental portrait of an open-ocean dispersal barrier for the marine plankton. Within all four Atlantic and Pacific subtropical gyres, we found a general lack of genetic subdivision among sites, as has been observed in a few other globally distributed plankton species.