It has been speculated that humpback whales, Megaptera novaeangliae, from the northeastern North Atlantic breed in tropical waters off the coast of West Africa and therefore that they represent a separate breeding population from that which winters in the West Indies. We determined the genotype at six microsatellite loci as well as the sequence of the first 288 nucleotides in the mitochondrial control region of 133 skin biopsies collected from humpback whales in the central North Atlantic (Iceland and Jan Mayen) and the northeastern North Atlantic (Bear Island and the northern coast of Norway). We detected no significant deviations from Hardy-Weinberg proportions nor any differences in genotype frequencies between localities at the nuclear loci. However, the mitochondrial analyses revealed two distinct matrilineal aggregations: the central and the northeastern North Atlantic. Our findings were not compatible with the idea of a separate eastern North Atlantic breeding ground unless one has been established recently. The proposed alternative hypothesis of a common North Atlantic panmictic population (wintering primarily in the West Indies) in which individual whales display maternally directed site-fidelity to specific feeding grounds was supported by re-sightings of two northeastern North Atlantic humpback whales in the West Indies.