The Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis) is a unique freshwater subspecies of Neophocaena phocaenoides, which is endemic to the Yangtze River of China and now is critically endangered. As one of the three possible effective conservation measures, an ex situ conservation breeding colony has been successfully established for the Yangtze finless porpoise in Tian-e-Zhou Baiji National Natural Reserve, located at Shishou City in Hubei Province. However, in the early spring of 2008, a large snowstorm, lasting several days, led to the death of several porpoises in the reserve. To estimate the genetic loss caused by the snowstorm, a batch of 18 species specific microsatellite markers were employed to investigate the genetic diversity of the colony before and after the snowstorm respectively. Besides, the computer software BottleSimV2.6, was applied to simulate the losing process of genetic diversity in the future. Results indicated that the Tian-e-Zhou ex situ conservation colony after the snowstorm still showed moderate level of genetic diversity (for 18 microsatellite loci, A=4.780, Ho=0.748, He=0.674). The snowstorm in 2008 did not cause severe genetic loss. Nevertheless, simulation results showed that genetic diversity of the Tian-e-Zhou ex situ conservation colony would decline rapidly in the future, if no effective measures were taken. Approximate 79% of the alleles and 84% of the heterozygosity would be reserved after 100 years. Simulations also indicated that lose of genetic diversity would be slowed down by increasing the population size and optimizing the sex ratio. Combining the simulation results from this study and the fact of rapid decline in wild population, the best ex situ conservation strategy for Yangtze finless porpoises living in the Tian-e-Zhou National Natural Reserve is to recruit suitable individuals from other wild populations, to establish a larger, more effective breeding population, with much greater genetic diversity.