Abstract: Pacific oyster(Crassostrea gigas)is a widespread,delicious and nutritious species and is of high economic value.The codominant molecular microsatellite marker(also called simple sequence repeat,SSR)complies with Mendelian inheritance principles and is a powerful tool for analyzing population genetic structure,breeding and constructing genetic map because of its highly polymorphic and accurate genotyping.Sequences used in the study were obtained from end sequencing of fosmid library of the C.gigas.TRF software was used to exploit SSR loci with dinucleotide repeat,and 50 pairs of primers were acquired based on conserved SSR flanking sequence.We did preliminary screening in eight individuals and 17 of the above 50 primers were proved polymorphic.These primers were then screened and verified in a wild population in Qingdao,Shandong Province.Of these loci,17 showed polymorphism.The average number of allele(N_a),number of effective alleles(N_e),observed heterozygosity(H_o),and expected heterozygosity(H_e)was 4,2.82,0.395 9,and 0.628 8,respectively.Among these loci,polymorphism information content(PIC)of 11 loci was more than 0.5,and 49 alleles in total were suitable for C.gigas population genetic structure analysis.The other 6 loci was moderately polymorphic and 0.25χ² test)and Sequential Bonferroni calibration,we found that all loci except DEC_1 deviated equilibrium,suggesting that the growth and frequencies of genotypes of C.gigas changed.Blastp alignment analysis of 10 000 bp flanking sequences of SSR loci in nr database of NCBI showed that 13 linked gene sequences were development or metabolism related and can be used as molecular markers.The present results indicated that the development of SSR molecular marker based on the fosmid library can effectively remedy the predicament of lacking SSR markers of Pacific oyster to provide basis to protect and utilize the genetic diversity of this species.