Studies on DNA microsatellites and a tagging programme both provide information on the degree of interchange of Dissostichus eleginoides (Patagonian Toothfish) between two sites 40 nautical miles apart near Macquarie Island. Five DNA microsatellite loci were identified that showed polymorphism levels appropriate for population structure analysis, and two of these gave results that suggest samples from the two sites are not homogeneous at the 5% probability level. While the other three loci did not demonstrate significant spatial heterogeneity, combined results across all five loci again indicated heterogeneity at the 5% probability level. Results from tagging experiments support the inference from the genetic analyses that interchange of fish between the two sites is very low. Of 469 recaptures at both sites combined, only one fish had moved between sites. As the DNA analysis has so far only been performed on small numbers of fish and loci these results must be regarded as preliminary, but if confirmed by further study the implication of very localised stocks of D. eleginoides will have a great effect on the management of commercial fisheries for this species.