To analyze the genetic diversity of natural population and select the specific microsatellite markers for identifying effectively genetic characteristics of population in Japanese flounder( Paralichthys olivaceus) in this study,seventy-four wild individuals captured from the Bohai Sea were used to form the experimental population.A set of 72 microsatellite markers located on different regions in linkage group were chosen to carry out the genetic analysis.In these markers,17 were located in the centromeric region,36 in the distant region from the centromere and 19 in the intermediate region of linkage groups.Analysis showed that the number of alleles(A)ranged from 6.400 to 7.389,number of effective alleles(N_e)ranged from 4.469 to 5.129 and Shannon’s information index(I)ranged from 1.565 to 1.683 in different regions of linkage group.The observed heterozygosity(H_o),unbiased expected heterozygosity(H_e)and polymorphism information content(PIC)was from 0.568 to 0.593,from 0.738 to 0.753 and from 0.707 to 0.746,respectively.The Hardy-Weinberg departure value(d)was lower than -0.200,while,genetic distance(GD)among individuals in population was above than 0.620.Each genetic parameter demonstrated that there was richer genetic diversity in experimental population and relatively farther genetic distance among individuals.This population was suitable for conducting selective breeding as founder population.Significant difference did not exist in the genetic parameters obtained by microsatellite markers located on different regions in linkage group,which verified that there was no necessary correlation between the positions of marker located and the degree of genetic diversity of markers.However,these polymorphic markers could be used as marker candidates to analyze the genetic structure in population of Japanese flounder.