refuse to eat dead prey or man-made feed. However, experiments with long-term cultivation suggest that can be domesticated to feed on inert baits. Selective breeding of using molecular markers and mass cultivation with artificial feed reduces the problems associated with cost, contamination, and disease. Pepsinogen is an acid gaster-digestion hydrolase which digests proteins under acidic conditions. Acidic proleases are sometimes used as additives in animal feed as they promote digestion and absorption of nutrients in fish. In order to search the distribution of the alleles and genotypes of pepsin gene () gene between domesticated and undomesticated populations, we identified SNPs in introns 5, 6, 7, and 8 and exons 6, 7, and 8 of the using DS, PCR-RFLP, and CRS-PCR. Two SNP sites (T1C, C52T) was identified in exon 7 of the gene, both of which were synonymous mutations. There was not significant difference in the occurrence of the SNPs between domesticated and undomesticated populations (>0.05). Five diplotypes were constructed based on two SNPs in the experimental population. There was a significant association between diplotype1 and diplotype5 in the two populations (<0.05). Our results provide a foundation for marker assisted selective breeding. The gene offers considerable potential as a candidate marker for the domesticated feeding phenotype in