Brucella ceti has been detected in several species of free-ranging odontocetes, in several geographic areas but it has not been reported in Indo-Pacific finless porpoises (Neophocaena phocaenoides) nor in any odontocetes in waters in the South China Sea. Sampling of odontocetes stranded in Hong Kong Special Administrative Region, People's Republic of China, was carried out as part of a stranding monitoring program to evaluate the pathogens harbored by these threatened species. A real-time PCR method targeting the Brucella genus-specific 31kDa Brucella cell surface salt extractable (bcsp31) gene, gene sequencing, and phylogenetic characterisation produced three PCR products of the expected size and sequence, from two stranded Indo-Pacific finless porpoises. The PCR products were obtained from brain tissue from of a neonate and from mammary fluid from a sexually mature female. Further testing for this pathogen should be performed to determine whether Brucella ceti might have a detrimental effect on reproduction and calf survival in Indo-Pacific finless porpoises and pose a threat to the conservation of this species. The importance of biosafety and biosecurity measures when handling cetaceans or their tissues and products in the South China Sea is also highlighted.