Sixty-five microsatellite markers（24 EST-SSRs markers and 41 SSR markers） were selected to analyze the genomic DNA of 84 progenies derived from the recombinant backcross lines （BC） of common carp，which came from the backcross between Barbless carp and Hebao-cold tolerance red carp. The results showed that a total of 182 different alleles were found，and the number of alleles in each locuswas 2 to 4. The DNA fragment length was 142 bp to 329 bp，and the number of valid alleles was 1.391 3 to 3.935 31. The value of observed heterozygosity was 0.321 4 to 1.000 0，expected heterozygosity was 0.282 9 to 0.753 5 and the mean polymorphism information content （PIC） was 0.512 0. A GLM procedure was used to analyze the correlation between the 65 microsatellites and body weight，length height and upper jaw length wensize. Results uncovered that HLJ852 had a significant impact on body weight，length and Upper jaw length wensize，and HLJ365 had a significant impact on body weight and height. HLJ816 had a significant impact on body weight and body height. HLJ726 had a significant impact body weight. HLJ107 and HLJ1098 had a significant impact on body length. HLJ111 and HLJ817 had a significant impact on body height. HLJE331，HLJ906 and HLJ330 had a significant impact on upper jaw length wensize. In addition，the genotypes of these correlative loci were investigated with the aid of mathematical modeling idea.