The finless porpoise (Neophocaena phocaenoides) inhabits a wide range of tropical and temperate waters of the Indo-Pacific region.Genetic structures in three populations of finless porpoises in Chinese waters (i.e.Yangtze River,Yellow Sea,and South China Sea) were studied,among which the Yangtze finless porpoise was widely known due to its highly endangered status and unusual adaptation to freshwater.To assist in conservation and management of this species,ten microsatellite loci were used to genotype 125 individuals in the populations above.Contrary to the low genetic diversity revealed using mtDNA control region sequences,relatively high levels of microsatellite genetic variation (HE=0.732-0.795) were found,comparable to other cetaceans.Bayesian clustering analysis suggested that finless porpoises in Chinese waters could be described as three distinct genetic groups,which well corresponded to previously defined three populations or subspecies based upon morphological variation and distributional pattern.Genetic differentiation was significant among populations with FST values ranging from 0.07 to 0.137.Immigration rates estimated using a Bayesian method and population ancestry analyses suggested no or very limited gene flow among populations even in the overlapped area between populations.These results strongly supported the classification of these populations into distinct evolutionarily significant units (ESUs) or subspecies,and therefore they should be treated as different management units (MUs) in designing conservation programme.