Abstract: Mandarin fish (Siniperca chuatsi, Basilewsky) has been one of the most important valuable domestic freshwater aquaculture fish in China. It is an important sedentary piscivorous fish in lakes adjacent middle and lower reaches of the Yangtze River. For many years of aquaculture, the germplasm quality and genetic diversity may have declined due to neglecting to inspect the genetic diversity in mandarin fish and the lack of the long-run and effective administer. In order to aid in investigation of the population genetic structure and marker assisted breeding, the genetic diversity and population structure of mandarin fish from the wild population and the artificial releasing population of Xiaosihai Lake were investigated by using microsatellite DNA markers. In total 68 individuals were all collected and consisted of 34 wild individuals and 32 artificial individual. The artificial individuals were tagged with CWT (Coded Wire Tags) when those been released one year ago. Genomic DNA was extracted from ethanol-preserved fin tissues by using phenol-chloroform method. Using a set of microsatellite primers originally reported in Mandarin fish (Siniperca chuatsi, Basilewsky), we carried out many cross-species PCR amplifications. PCR products were separated on 7.5% nondenaturing polyacrylamide gels, stained with ethidium bromide in water and visualized with ultraviolet. The data were calculated and analyzed by statistic method. The results indicated that 50 alleles were found in ten microsatellite loci in two populations. The number of alleles per loci ranged from 2-3 and total number was 22 in artificial releasing population; in wild population, the number of alleles per loci ranged from 3-5 and 37 in total. Polymorphism information content value (PIC) was higher and more than 0.5 in locus SC13, SC19, SC23, SC29, SC34 and SC42 in Xiaosihai wild population; meanwhile the artificial releasing population had the lower PIC value, only one locus more than 0.5 in SC31. The average PIC value from wild and releasing population were 0.5188 and 0.4071 respectively. The observed heterozygosity (Ho) and the expected heterozygosity (He) were calculated based on frequencies of genotypes and alleles of each microsatellite locus, the average He value was higher in wild population (Ho =0.8588, He =0.6096) and lower in artificial releasing population (Ho =0.8750, He =0.5210). The results showed that the genetic diversity of wild population was more sufficient higher than that of the cultured population. Genetic differentiation and hierarchical partition of genetic diversity were evaluated by Fst, which indicated that the gene differentiated more seriously apparently between wild and stocking population. After it being checked by χ2 test of the Hardy-Weinberg Equilibrium (HWE), most loci were found to be significantly deviated from HWE (P<0.001) in the two populations in which heterozygote excess was apparent. The present study results revealed inbreeding and the bottleneck effect as the main causes which result in genetic differentiation between the two populations. All of these indices indicated that the artificial releasing population of mandarin fish have relatively low genetic diversity. The reasons may result from inbreeding while artificial propagation, and neglecting the genetic diversities and population quantity while carried out artificial releasing program. The consequent of CWT tagged in juvenile mandarin fish and theoretical signification to other settlement fish were also discussed.