Located at the confluence of the East China Sea and the Yellow Sea, the Yangtze River Estuary is the area of overlapping distribution for two subspecies of the narrow-ridged finless porpoise (Neophocaena asiaeorientalis).In recent years, finless porpoise deaths occur frequently in this area, which has aroused widespread concern of the public.In this study, the genetic diversity and population dynamics were investigated using 16 polymorphic microsatellite loci in 36 samples of the East Asian finless porpoise (N. asiaeorientalis sunameri) from the Yangtze River Estuary. The results showed that 14 microsatellite loci did not deviate from Hardy-Weinberg equilibrium except for 2 loci. A total of 129 alleles were obtained in all of 16 loci with an average number 8.1. The average of observed heterozygosity (Ho) was 0.733; the average of expected heterozygosity (He) was 0.758, and the value of the polymorphism information content (PIC) was above 0.5. The level of genetic diversity is similar to marine mammals such as the Indian-Pacific finless porpoise(N. phocaenoides) and the seal (Phoca largha), but significantly higher than valuable terrestrial mammals such as the giant panda (Ailuropoda melanoleuca) and the Amur tiger (Panthera tigris altaica). In addition, the heterozygosity excess test and Mode-shift analysis showed that the population has not experienced genetic bottleneck effects during the recent historical period. Meanwhile, 4 simulations on Msvar software exhibited virtually no detectable effective population size change in their recent past, and estimated the recent effective population size about 5 623 individuals, which revealed that the population of N.asiaeorientalis sunameri is large and stable in the Yangtze River Estuary.