in 1998 in China. To protect and exploit this endangered species effectively, investigations on population structures, resources and artificial reproduction have been conducted. However, seldom study was reported in analysis of population genetic structure using molecular markers. In this study, 17 microsatellite markers were used to analyze genetic diversity and structure of 4 populations of Taimen from Heilongjiang River, named Huma population (HM), Hutou population (HT), Haiqing population (HQ) and Zhuaji population (ZJ), separately. Statistical results showed that each population was on a mediate level in genetic diversity, and the genetic diversity level of Taimen had a positive correlation with population size, which presented a declining trend annually. The analysis of population genetic structure showed that there existed remarkable genetic differentiation among the 4 populations. Taimen in Heilongjiang River was divided into two genetic types, HM type and WSL type, and WSL type was further subdivided. The small size of effective population was caused mainly by the changes of population number and the genetic bottleneck, which led to greater inbreeding pressure within populations. Through the examination of recent and long-term gene flows for River, we found that immigratory rate and migratory rate in each population were asymmetrical, and the large population migrated to the small population. The values of recent gene flow were smaller than those of long-term gene flow, indicating that gene exchanges were blocked due to the harsh environments and shrunk population censuses. According to the above mentioned, we thought that the harsh environments and the decreased population number caused the degradation of genetic diversity, the divergence of genetic structure, the occurrence of genetic bottleneck, the small size of effective population and the obstacle of gene flow amongst populations. Overall, Taimen in Heilongjiang River should be preserved comprehensively as an endangered fish species