Abstract: Study on the genetic diversity and Population genetic characteristics of Hypophthal michthys molitrix between wild and stock enhancement in the Poyang Lake water system using by PCR and DNA sequencing. Complete sequences of the mitochondrial DNA control region (935bp) of 54 silver carps from Ruichang( RL),Gan river (RL) and stock enhancement (SL) were directly sequenced, of which 3 gaps , 41 variable sites and all parsimony –informative sites were detected in 24 haplotypes. The average ratio of transitions vs transversions was 14.344. In the neighbor-joining tree individuals from various localities were intertwined without genealogical and geographic clusters. The analysis of molecular variance (AMOVA) showed that the variation was from the within population, FST=0.22388 also indicated that the genetic variation was from within the population mainly. Genetic distances among 3 populations were 0.01035～0.01634, and Fst value were 0.08252～0.39171, indicating that between the three population groups were significant genetic differentiation. The haplotpic diversity of wild and stock enhancement of silver carps were 0.727、0.978 and 0.947,respectively, Their The haplotpic diversity of GL,RI and SL population were 0.00897、0.01135 and 0.00978, respectively. As silver carps in Ruichang were composed of the most abundant genetic diversity in the 3 sampled sites, secondly was population of stock enhancement, The haplotpic diversity and haplotpic diversity of Gan river population were the very lowest , Gan river should be as priority conservation areas.