The Yangtze finless porpoise, Neophocaena phocaenoides asiaeorientalis, is an endangered small cetacean that occurs only in the middle and lower reaches of the Yangtze River of China. The establishment of a breeding population of the porpoise in Tian-e-Zhou Baiji National Natural Reserve represents the first attempt at ex situ conservation efforts for a cetacean species. With the goal of effective protection, management, and monitoring of this preserved population, we examined its genetic diversity using 930 bp of mtDNA control region sequences and 13 polymorphic microsatellite loci. A very low level of genetic variation (h = 0.6010 ± 0.0029 s.d.; π = 0.0007 ± 0.0000002 s.d.) in the mtDNA control region sequences and a moderate genetic diversity (Ho = 0.5740 ± 0.2575 s.d.) in the microsatellites were detected in the population. It is necessary to introduce more individuals with representative genetic variations into the reserve in order to form a larger and healthier group structure for long-term survival of the population. Successful establishment of the Yangtze finless porpoise population in the Reserve also provides a useful model for an ex situ conservation programme for other rare and endangered species.