Molecular markers were employed to investigate the fine-scale stock structure of Patagonian toothfish in the west Indian Ocean sector of the Southern Ocean. Four collections of toothfish from the Kerguelen (n=1), Crozet (n=1) and Prince Edward and Marion (n=2) Islands were typed genetically using two fragments of mtDNA and seven nuclear microsatellite loci. MtDNA haplotype diversity was moderate; ranging from 0.331 to 0.343. Allelic variation at the seven microsatellite loci was widespread with observed heterozygosities per locus per collection ranging from 0.000 to 0.900 and allele counts from 1 to 21. There was no evidence for significant mtDNA heterogeneity among the four collections and only weak and inconsistent heterogeneity (based on minor allele frequency differences) at several microsatellite loci among the four collections. Both mtDNA and microsatellite FST values indicated no population sub-structuring among the collections. Genetic variance estimates of both mtDNA (?ST=-0.016) and microsatellites (?ST=-0.005) indicated all variation was seen within the toothfish collections. Comparisons with previously collected genetic data from Heard and McDonald Island collections (n=4) also showed a lack of genetic differentiation among the geographic groups, indicating significant gene flow among west Indian Ocean sector fishing locations.