Abstract: Ten microsatellite loci were selected to analyze the correlation with quantitative trait locus of body weight and length genomic of Apostichopus japonicus using single marker-based analysis.DNA of 60 eight months old individuals of Apostichopus japonicus which have differences in growth traits were analyzed by 10 microsatellite markers.The results showed that a total of 50 different alleles were found,the number of alleles in each locus was 3 to 7,and the number of mean valid alleles was 5.0.The polymorphism information content(PIC)of ten microsatellite loci was 0.083 3 to 0.666 7,and the value of heterozygosity was 0.236 1 to 0.767 7,which proved the ten loci can be adopted to make correlation analysis.SPSS program was used to analyze the effects of these 10 microsatellites on body weight and length of Apostichopus japonicus.The results showed that AB,AD and CD genotypes of AjSSR02 had significant difference in body weight and length with other types,allele A of AjSSR04 played a positive role in both body weight and length,FF genotype of AjSSR06 had a significant impact on weight but not on length,and A and B allele of AjSSR09 played positive and negative roles in growth traits respectively.