Abstract: The sinipercine fishes,belong to a group of the lower percoids,have a geographical distribution in East Asia and dwell in lakes and rivers system,of which most species are in China.The mandarin fish (Siniperca chuatsi) is a very popular food in China.It has become one of the important aquaculture species and there is considerable expertise in its culture.The aim of this study was to explore the relationship between environment and the genetic background of S.chuatsi populations and their genetic differentiation,thus provided information and theoretical basis for artificial releasing in a large area,also in the development and utilization of germplasm resources of S.chuatsi.Ten Simple Sequence Repeat (SSR) markers were used to compare genetic diversity among seven S.chuatsi populations which were consisted of Yangtze Rive,Yangtze River-connected lakes (Dongting Lake and Poyang Lake); Yangtze River-disconnected lakes with stocking (Tangxun Lake,Zhangdu Lake and Niushan Lake) and Yangtze River-disconnected lake without stocking (Xiao-Sihai Lake),all samples collected on the fishing boat directly.Observed heterozygosity (Ho),expected heterozygosity (He) values,polymorphic information (PIC) and number of effective alleles (Ne) were all determined.The results showed that S.chuatsi has a certain genetic diversity although some rare polymorphic loci were missing.The observed genetic diversity was in the order: Yangtze River,Yangtze River-connected lakes>Yangtze River-disconnected lakes without stocking > Yangtze River- disconnected lakes with stocking.In the study,some rare alleles were found disappeared in Yangtze River- disconnected lakes.157 alleles were found in the 7 populations by using 10 primers,the number of alleles in populations of XSH,NS,ZD,TX,YZ,DT and PY was 37,32,29,25,62,67 and 76,respectively.The PIC values among 7 populations varied from 0.4240 to 0.7322.At the same time,the lowest values was found in TX population while the higher values were found in Yangtze River,Yangtze River-connected lakes (DT and PY populations),the values were 0.7002,0.6907 and 0.7322 respectively.This result suggested that as artificial interference pressures increased,the change of genetic diversity decreased.After it being checked by χ2 test of the Hardy-Weinberg equilibrium (HWE),most loci were found to be significantly deviated from HWE (Pst) was 0.2727,which showed small partial genetic diversity (27.27 %) present among populations.Gene flow (Nm) between primers varied from 0.4677 to 0.9467 and the mean Gene flow (Nm) was 0.6669.The results showed geographic isolation as the main reason for genetic differences between Yangtze River-connected lakes and disconnected lakes.The UPGMA cluster figure that was constructed based on the genetic distance matrix showed seven populations that became genetically closer at each step.The first group was the YZ and PY populations and the closed together with DT (Yangtze Rive,Yangtze River-connected lakes) population,group two consisted of the XSH population and the NS population,group three was the ZD and TX populations.Analysis also showed that genetic diversity in non-stocking population was higher than those of stocking populations,which indicated that artificial releasing also resulted in genetic differentiation.The results of the study have important implications for the stock management of S.chuatsi populations in shallow lakes along the middle reaches of the Yangtze River.