Using 30 microsatellite markers and combining quantity characters such as body weight, body size and body width, we evaluated the genetic potential of 3 Germany mirror carp populations. Number of effective alleles (Ae), observed (Ho) and expected (He) heterozygosity values and polymorphic information contents (PIC) were all calculated. 287 alleles and 559 genotypes were detected. The DNA fragment length was 109-400 bp. The Hardy-Weinberg Equilibrium was checked and phenomenon of some disequilibrium were studied according to the test of c2. The result showed that the level of genetic variability was moderate, but genetic potential of Shuanglai population was much lower than that Huanxin and Songpu breeding populations. Polymorphic Information Contents (PIC) of the 3 populations of Germany mirror carp were between 0.08787 and 0.5377, both of highly and moderately polymorphic markers were 13. The number of effective alleles (Ae) were between 1.1014 and 6.4665. The observed (Ho) and expected (He) heterozygosity values were 0.0968-0.9892 and 0.0926-0.8554 respectively. The linkage correlation was analyzed using data of body weight, body size and body width and 30 loci. The result shown that there existed 2 loci, HLJ319 and HLJ693 associated with body size. The HLJ693 locus significantly correlated with body weight character. The HLJ677 locus linked with body width. And then the result were verified in Recombinant Inbred Lines (RIL) of common carp. It shown that the HLJ319 locus was significantly linked with body size, the same as the result of common carp QTL location.