Application of microsatellites in the Yangtze finless porpoise ( Neophocaena phocaenoides asiaeorientalis) has not been reported. In this study amplification of microsatellites were performed in DNA samples of the Yangtze finless porpoise population by PCR using twenty-three published microsatellite primers from Phocaena phocoena, Eubalaena glacialis, Physeter catodon, Megaptera novaeangliae, Tursiops truncates, Globicephala melas. The results indicated seven primer pairs produced stable and polymorphic PCR products in the population. Further sequencing analysis showed that the amplified product sequences of the seven primer pairs all own AC or GT di-nucleotide repeats, which confirmed that the amplification was valid. The results suggest that applicable primers in fingerprinting analysis of the Yangtze finless porpoise could be obtained faster by screening of microsatellite primers isolated from other cetacean species.