The Black-footed Albatross Diomedea nigripes is an endangered seabird that is endemic to the North Pacific. The genetic structure of Black-footed Albatross populations on three of the Hawaiian Islands and on Izu-Torishima Island, Japan, has been studied previously, using the mitochondrial cytochrome b region. Hawaiian and Japanese breeding groups are genetically different, and the genetic diversity of the birds on Izu-Torishima is lower than that of birds in the Hawaiian Islands. We analyzed 50 Black-footed Albatrosses from the Bonin Islands, where a relatively stable population persisted throughout the twentieth century. Although albatrosses in the Bonin Islands do not differ significantly from those on Izu-Torishima in their cytochrome b region sequences, they do exhibit higher genetic diversity (as high as those from the Hawaiian colonies). A statistical parsimony network revealed two clades, one primarily in the western North Pacific colonies and the other primarily in eastern North Pacific colonies. The total network appears as a dumbbell-shaped phylogeny, suggesting recent population expansion in both populations, although the population breeding in the western North Pacific is only about 5% of the size of that in the eastern North Pacific. Our results suggest that Black-footed Albatrosses in the Bonin and the Hawaiian Islands differ genetically but are comparable natural biological units for conservation and management purposes.