Microsatellite DNA markers are increasingly being used to improve selective breeding programs. Currently, there is a need for molecular markers associated with traits for marker assisted selection in shrimp breeding programs. We analyzed the association between microsatellite DNA markers and body length, total body height, and body weight in an F2 family of Chinese shrimp (Fenneropenaeus chinensis) that were mated by artificial insemination. Eighty individuals from the F2 family were chosen for the normal distribution test. Nineteen microsatellite primer pairs were obtained to amplify the total DNA and genotype each locus. We calculated the mean number of alleles, mean expected heterozygosity, mean polymorphic information content. Genotypic differences of these microsatellites loci between the maximal high group and minimal low group were analyzed using SPSS11.5 software. One-way ANOVA was conducted to test the association between the individual marker alleles and the three economic traits. The body length, total body height, and body weight were normally distributed(P>0.05). The mean number of alleles, mean expected heterozygosity, and mean polymorphic information content were 2.470, 0.533 and 0.442, respectively. The microsatellite loci RS0683 and FC019 were significantly associated with body weight, body length, and total body height (P<0.05 or P<0.01). The most favorable genotypes for growth traits at the microsatellite locus RS0683 was AA (P<0.01) and the most unfavorable at locus FC019 was AA (P<0.05). We speculate that the genotype AA was positively associated with the three economic traits at locus RS0683 and the genotype AA was negatively associated with the traits at locus FC019. Our results suggest that selective genotyping integrates the advantages of BSA and marker-based analysis to improve our ability to detect an association between quantitative trait locus and markers. Two of the microsatellite loci had a significant effect on the three economic traits. Identification of a large number of DNA markers linked to QTL controlling the resistance to WSSV will contribute to the application of DNA marker-assisted selection during breeding of Chinese shrimp for intensive culture