The mackerel icefish (Champsocephalus gunnari Lönnberg E (1905) The Fishes of the Swedish South Polar Expedition. Wiss. Ergebnisse Schwedische Südpol- Exped. 1901–1903, vol 5, p 37 is widely distributed south of the Antarctic convergence and over shelf areas surrounding sub-Antarctic Islands. In order to evaluate global population structure in this species, we examined DNA sequence variation in four mitochondrial regions and four nuclear genes in icefish 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 remaining Atlantic populations (Shag Rocks, South Georgia, and Bouvet Island). The mitochondrial and nuclear SNP markers developed here will be useful for more extensive analyses of population structure in this species.