Large-scale transport of seawater in ocean currents may generate spatially complex population structure through the advection of life stages of marine fish species. To test this, we compared the chemistry of otolith nuclei from Patagonian toothfish (Dissostichus eleginoides), presently managed as spatially discrete populations corresponding to fishery management areas along the Antarctic Circumpolar Current (ACC), which transports water eastward around the Southern Ocean. The chemistry of otolith nuclei, laid down during early life, differed significantly between fishing areas off South America and the Antarctic and between some Antarctic areas. We also found evidence of four groups of fish with different early life chemistry: one associated with South America and three Antarctic groups showing mixing consistent with advective transport along the ACC. These results suggest that toothfish populations are structured by their physical environment; population abundance and persistence may rely on a restricted number of breeding members with access to spawning grounds, whereas fisheries may rely substantially on nonbreeding vagrants transported from fishing areas upstream.