The Antarctic toothfish, Dissostichus mawsoni, serves as valuable fishery resources around the Antarctic Continent since 1997, managed solely by the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR). Although defining genetic or stock structure of populations is crucial for improving fishery management of this species, the number of populations or stocks of D. mawsoni in this Antarctic region remains currently unknown. In the present study, we assess the population genetic and phylogeographic structure of the Antarctic toothfish populations across 11 geographic localities from the two main Subareas 88 and 58, based on a combined analysis of mitochondrial DNA (mtDNA) cytochrome oxidase I (COI) sequences and four nuclear microsatellite loci. MtDNA revealed a very low level of polymorphism (h=0.109, π=0.0002) with only eight COI haplotypes in 213 individuals, connected only by 1-3 mutational steps. Nonetheless, microsatellites showed much higher variation with allelic richness (AR) values of 5.8 to 6.7 within populations. Four of six populations showed a genetic signal of inbreeding, despite no sign of population bottlenecks detected. Population structure analyses of microsatellites suggest that the sampled 88 Subarea populations are likely to comprise a well-admixed single gene pool (one genetic stock). However, given weak but significant microsatellite differentiation found between some populations, the possibility of existence of multiple stocks could not be fully excluded. To clarify this, further study with additional polymorphic markers (such as microsatellites) using more samples from other areas, particularly the 58 Subarea will greatly help to determine the population or stock structure of D. mawsoni in this region. The findings of this study will inform conservation efforts on the stock (unit) management for this valuable fishery resource.