The Southern Ocean constitutes ten percent of the world's ocean. It contains 322 species of fish, a small number in relation to the global diversity of 25,000 to 28,000 species. The high degree of species level endemism in the Southern Ocean is an indication of a long period of evolution in isolation.

The mackerel icefish (Champsocephalus gunnari Lönnberg 1905) is widely distributed south of the Antarctic convergence and over shelf areas surrounding sub-Antarctic islands. In order to evaluate global population structure, I examined DNA sequence variation in four mitochondrial regions and four nuclear genes from four locations in the Atlantic Ocean sector and one location in the Indian Ocean. Despite small sample sizes, mitochondrial and nuclear gene data indicated the existence of at least three genetically distinct stocks: Heard Island, South Shetland Islands, and the south Atlantic.

The Antarctic toothfish (Dissostichus mawsoni) exhibits a circumpolar distribution in coastal waters south of the Antarctic convergence. In order to evaluate population structure, I examined DNA sequence in four mitochondrial regions and thirteen nuclear genes in samples from four CCAMLR Subareas in the Southern Ocean Significant genetic differentiation within and among locations was observed for both mitochondrial and nuclear loci.

The Patagonian toothfish (Dissostichus eleginoides) exhibits a circumpolar distribution in the Southern Ocean and is found largely north of the Polar Front. In order to evaluate global population structure, I examined four mitochondrial regions and 13 nuclear genes in 1221 samples from 42 locations. Geographic variation in selected mitochondrial and nuclear single nucleotide polymorphisms revealed substantial heterogeneity in the Southern Ocean. Both mitochondrial and nuclear DNA showed significant differentiation between South America and Antarctic collections, but the magnitude of the differentiation was significantly greater in mitochondrial DNA (82% of the total variation occurring between the two regions compared to 1% for nuclear DNA). Levels of mitochondrial and nuclear gene diversity were much higher in D. eleginoides than in its congener, Dissostichus mawsoni. Finally, DNA sequence analysis of a lone Patagonian toothfish caught off Greenland placed it among the South Atlantic assemblage.