Humpback whales (Megaptera novaeangliae) have a worldwide distribution in the oceans and are known for their very long migratory potential. Their migration routes consist of productive feeding areas located in high-latitudes and to low-latitude areas used as breeding and calving grounds. Genetic studies in humpback whale populations consist mainly of nuclear and mitochondrial DNA. In general, these studies provide similar results to estimates of gene flow, but some discrepancies may be caused by gender-biased migration to breeding grounds and further dispersion by males. There is little evidence of trans-equatorial and inter-oceanic migrations, but those movements have been confirmed by both analysis of photo-ID of naturally marked individuals and also genetic analysis. The combination of migratory and genetic analyses suggest an overlapping of breeding grounds in low-latitude areas, where the gene flow among those oceanic populations is more likely to happen, despite the opposite seasons in the northern and southern hemispheres. These results have important implications in the conservation perspective, especially for the determination of protected areas and for development of international agreements.