The taxonomic status of humpback dolphins (genus Sousa, sub-family Delphininae) is unresolved. While the classification of this genus ranges from a single to three nominal species, the International Union for Conservation of Nature and the International Whaling Commission only recognise a 'two-species' taxonomy (S. teuszii in west Africa, and S. chinensis in the Indo-Pacific). Under the IUCN (2008), S. chinensis is listed as 'near threatened', but is only considered as a 'migratory' species in Australia. Taxonomic resolution of the genus Sousa is needed to define particular conservation status and develop appropriate management actions. Using phylogenetic analyses of 1,082 bp of mitochondrial and 1,916 bp of nuclear DNA, we provide multiple lines of genetic evidence for the genetic distinction of S. chinensis in China and Indonesia from S. chinensis in Australia. The separation of Australian Sousa from Sousa of Southeast Asia requires a review of their current conservation status and respective management actions.