Abstract: Siniperca scherzeri Steindachner,a high-valued freshwater fish,is endemic in East Asia.However,its natural resource has declined by the destruction on its ecological environment and excessive capture in fisheries.To investigate and understand its overall genetic background,genetic characteristics and divergences of Siniperca scherzeri Steindachner from Yalujiang River,Haihe River,Yangtze River,Qiantangjiang River,Minjiang River and Xijiang River were analyzed by AFLP methods.Eight primer pairs were selected from 64 EcoRⅠ/MseⅠ primer combinations and used for further practical AFLP analysis.Total 211 bands were scored in 65 individuals with 126 polymorphic bands(59.7%),some population specific bands were also observed.The genetic variation of Yangtze population was the highest(6.7%) among 6 populations,and genetic distances of inter-population were higher than that of intra-population.The analysis of molecular variance(AMOVA) showed that there was significantly genetic differentiation among 6 populations(pS.scherzeri in China maybe resulted from accumulation of a large numbers of mutations under wide distribution ranges in different ecosystems.Genetic divergence among 6 geographical populations are significant,moreover,the genetic relationships are consistent with their geographical distribution.The formation of Qinling Mountains,which lies across the central China from west to east,was invoked to explain the distinct divergence between the northern group and the southern group.