In order to establish an SNP (single nucleotide polymorphism) acquisition system for the (insulin-like growth factor 2) gene, a total of 33 DNA samples extracted from 10 different carp species were sequenced and the data were analyzed to verify the function and efficacy of the breeding process for the new Huanghe carp strain. By determining the position and distribution of SNPs on the genome and obtaining the gene by segmentation at the genomic DNA level in this way, the applicability of primers from different carp species for use in Huanghe carp new strains was verified. As a result of the segmentation at the genomic DNA level, eight pairs of polymerase chain reaction (PCR) primers were obtained, and the corresponding SNPs were determined by direct sequencing and restriction fragment length polymorphisms. Furthermore, direct sequencing showed a single band from the PCR of Huanghe carp and Jian carp as well as the progenies resulting from their reciprocal crosses, which allowed us to confirm the validity of the target fragment. Finally, analysis of the Huanghe carp body weight data combined with the latest results allowed the detection of an SNP significantly associated with the body weight using primers. Likewise, another SNP was detected in association with the expression level of this gene. The methods used in this study were able to detect the SNPs of genes in the molecular breeding of carp within the range of the whole genome, to verify that the mutation at the No. 227 site on the primer of Huanghe carp led to reduced body weight, and to identify another SNP related to the expression level of IGF2b. This will provide the background for the study of polymorphic molecular markers and other functional genes in other species.