Water transported by the Antarctic Circumpolar Current (ACC) in the Southern Ocean may provide opportunities for Patagonian toothfish (Dissostichus eleginoides) to move downstream between island groups with little energetic cost, and may constrain movement in other directions, influencing population structure and richness. To test whether toothfish stocks were connected or segregated, we used an integrated experimental design to compare age-at-length data sampled at similar times from longline fisheries off the southern South American continent around the Falkland Islands north of the Sub-Antarctic Front of the ACC, and off Kerguelen and South Georgia Islands, situated respectively in the southern Indian and Atlantic Oceans to the south of the Polar Front. We fitted von Bertalanffy (VB) models representing segregation and coupling between management areas to the data, and tested between the models using a likelihood method. Toothfish showed significant differences in VB parameters between the Falkland Islands and both South Georgia and Kerguelen, but no differences between South Georgia and Kerguelen. This evidence suggests that, consistent with the dynamic-physical structure of the ACC, toothfish off the Falkland Islands are segregated from toothfish caught in the other two management areas, but that toothfish stocks at South Georgia and Kerguelen may be connected. Taken with the published genetic data, this evidence strongly suggests that toothfish population structure is related to the physical structure of the ACC and its fronts; that some toothfish populations may be connected between the major Southern Ocean basins; and that consequently, changes in toothfish population dynamics within one management area may have broader impacts through the Southern Ocean.