132 SSR and 63 EST markers were used to analyze the genotype of eightyfour individuals which crossed from barbless carp(Cyprinus pellegrini)and Hebao cold tolerance red carp(Cyprinus carpio var.wuyuanensis).The results showed that a total of 565 different alleles were found,and the number of alleles in each locus was 2 to 4.The DNA fragment length was 72 bp to 784 bp,and the average number of alleles per locus was 2.897 4.The mean polymorphism information content(PIC)was 0.584 9,and the average heterozygosity was 0.592 8.The GLM procedure was used to analyze the effects of these 195 microsatellites on body weight,length,head length and caudal peduncle length.Results revealed that HLJ133,HLJ346,HLJ360 were discovered very significantly related to carp’s body weight,HLJ133,HLJ368,HLJ390,HLJ673,HLJE96 had a significant impact on carp’s body length.Markers HLJ133,HLJ346,HLJ360 were discovered very significantly related to carp’s head length,and HLJ529,HLJE538,HLJE586 had a significant impact on carp’s head length.HLJ673,HLJE282 were discovered very significantly related to carp’s caudal peduncle length,and HLJ348,HLJ368,HLJ382,HLJ437,HLJ483,HLJ752,HLJE169,HLJE586 had a significant impact on carp’s caudal peduncle length.In addition,the correlation coefficient and the path coefficient were obtained between length,head length,caudal peduncle length and body weight.And the correlation between caudal peduncle length and body weight was insignificant.