Molecular markers were used to investigate the stock structure of Patagonian toothfish (Dissostichus eleginoides) in the West Indian Ocean sector of the Southern Ocean. Four collections of D. eleginoides from Kerguelen (n = 1), Crozet (n = 1) and Prince Edward and Marion (n = 2) Islands were typed using two fragments of mitochondrial DNA (mtDNA) and seven nuclear microsatellite loci. MtDNA haplotype diversity ranged from 0.331 to 0.351. Observed heterozygosities per locus per collection ranged from 0.000 to 0.900 and allele counts from 1 to 21. There was no evidence of significant mtDNA heterogeneity among the four collections and only weak and inconsistent heterogeneity (based on minor allele frequency differences) at three microsatellite loci among the four collections. Neither mtDNA nor microsatellite F_ST values indicated population sub-structuring among collections. Genetic variance estimates of both mtDNA (F_ST = –0.016) and microsatellites (F_ST = –0.005) indicated all variation was seen within collections. Comparisons with previously collected genetic data from Heard and McDonald Island collections (n = 4) were not significant among the geographic groups (mtDNA Ф_CT = –0.003; microsatellite Ф_CT = 0.004), indicating a lack of genetic differentiation among these West Indian Ocean sector fishing locations.