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Humpback whales ( Megaptera novaeangliae) in the Southeastern Atlantic Ocean (International Whaling Commission 'Breeding Stock B'-BSB) are distributed from the Gulf of Guinea to Western South Africa. Genetic data suggest that this stock may be sub-structured, but it remains unknown if this is due to reproductive segregation. This paper evaluates the spatial and temporal population structure of BSB humpback whales using a combination of maternally and bi-parentally inherited markers. The genetic differentiation that we identify in this study could be due to a combination of (1) spatial and/or temporal segregation on breeding grounds in the greater Gulf of Guinea, (2) the possibility of maternally inherited site fidelity to specific feeding grounds and (3) the use of two generalized but exclusive migratory routes (coastal and offshore) between feeding and breeding areas. Further, photo-identification and genetic sampling efforts in other areas of the Sub-Saharan Western Africa winter range and targeted deployment of satellite tags would help to clarify some of the apparent complexity in the population structure of animals biopsied in this region. [ABSTRACT FROM AUTHOR]