Abstract: Mirror carp (Cyprinus carpio L.) is one of the most important traditional domestic freshwater aquaculture fish in China. The seeding of mirror carp for aquaculture has come from the Heilongjiang River because germplasm resource of mirror carp is superior to those from other rivers and lakes. But advanced biological characteristic for aquaculture germ-plasm of mirror carp was obviously decreased during past years after multigene rations artificial propagation. The growth be-came slowly and the ability of antidisease reduced. Therefore, it is necessary to analyze and study genetic diversity and cor-relation analysis of microsatellite DNA markers with economic characters in mirror carp. In the present study, the genetic diversity and population structure of mirror carp from Heilongjiang River system were investigated using microsatellite DNA markers.The genetic examination on 24 microsatellite markers and combined quantity characters such as the body weight, body length and full length was carried out among the random samples in two semi-sib families of mirror carp, a total of 57 different alleles were found and the number in each locus ranged from 1 to 6. The average number of alleles was 3.21. The DNA fragment lengths were from 134 bp to 371 bp. In the two semi-sib families, the number of mean valid alleles (Ne) was 1.00 to 2.89, the value of average observed (Ho) and expected heterozygosity (He) ranged from 0.00 to 0.83 and 0.00 to 0.66, respectively, and the mean PIC was 0.00 to 0.58. The result showed that the level of genetic variability was moderate. Chi-square test was used to analyze the genotypes based on Hardy-Weinberg equilibrium, the P value deno-ted that the 2 families deviated equilibrium partially.A GLM procedure was used to analyze the effects of these 24 microsatellites on economic characters. Results uncov-ered that there existed 4 loci, HLJS19, HLJ848, HLJ855 and HLjE8, which had a significant impact on body weight (p<0.05). The HLJ519, HLJ848 and HLJ855 loci correlated with length and full length character significantly (p<0.05). Genotypes of that favorably affect economic characters were determined. Multiple comparisons of economic characters among microsatellite loci genotypes showed that allele 281 in locus HLJ519, allele 279 in locus HLJ848, allele 209 in locus HLJ855 and allele 189 in locus HLJE8 closely linked to the major gene related to body weight, body size and whole size of economic characters in mirror carp.