This study extends previous phylogeographic genetic studies of the Black-browed and Wandering Albatross species complexes through the addition of newly acquired genetic data from wandering-type albatrosses on Macquarie Island and Black-browed Albatrosses (Thalassarche melanophrys) on Macquarie Island and the Chilean islands of Diego de Almagro and Ildefonso. DNA sequencing of Domain I of the mitochondrial control region showed that the wandering-type albatrosses on Macquarie Island belong to the Diomedea exulans group and show close genetic affinity to populations on the Prince Edward and Crozet Islands. The populations of Black-browed Albatrosses on Diego de Almagro, Ildefonso and Macquarie Islands all fell into a distinct grouping that also included birds from Diego Ramirez, South Georgia and Kerguelen Islands. Both the Wandering and Black-browed species complexes show multiple distinct lineages, some with disjunct geographical distributions. We suggest that this is a consequence of prolonged isolation of populations during the Late Pleistocene followed by range expansion of D. exulans and T. melanophrys after glacial retreat from many subantarctic islands. Both species most likely dispersed from populations centred in the southern Indian Ocean.