The genetic structure of one breeding population of mirror carp(Cyprinus carpio L.) was analysed using thirty-five polymorphic microsatellite markers. The effective number of alleles (Ae), observed heterozygosity (Ho), expected heterozygosity (He) and polymorphism information content(PIC) were all determined. The Hardy-Weinberg equilibrium was checked by chi-square test. For each locus, 2-7 alleles were detected, with a total of 118 alleles for 35 loci . The value of Ae, Ho, He and PIC showed that the genetic variation of the population was not high .The average effective number of alleles and the mean polymorphism information content were 2.16 and 0.42, respectively, and the observed and expected heterozygosity were 0.431 and 0.4736 , respectively.The probability value of chi-square test showed that more than half of the thirty-five loci have significantly (Plt;0.01) deviated from Hardy-Weinberg equilibrium. The correlation of genotype of each locus and individual phenotype data was analysed , and 4 loci seemed associated with body weight and body size . When compared with the result of QTL mapping of common carp, HLJ319 locus was consistent with the mapping result approximately, which was significantly correlated with body size . Several significantly deviated loci were also analysed, and the possible cause of the kind of deviation was discussed .