Mandarin fish is one of the most commercially important freshwater fish in Chinese aquaculture. Once the fry of mandarin fish start feeding, in the wild they exclusively eat live prey fish; therefore in cultivation they refuse dead prey fish or artificial diets, contributing to the challenges of breeding this fish. Currently, the source of live feed for the intensively cultured mandarin fish is also cultivated. The challenges in cultivating live feed for mandarin fish include extremely high cultivation costs, difficulties in maintaining stock supply all year round, and disease prevention, which is very difficult in the cultivation process. Therefore introducing artificial diets in domesticated mandarin fish could resolve these challenges. Based on the existing research, this study analyzed the transcriptome data of mandarin fish, and the differences in expression of pepsinogen (pep and are considered as candidate genes for food habit traits in domesticated mandarin fish. In this study, single nucleotide polymorphisms (SNPs) on candidate genes were sequenced and typed in a feeder group fed dead prey fish diets and a non-feeder control group, and evaluated for associations with food habit domestication traits in 103 mandarin fish. The feeder means the fish accepts dead prey fish, and the non-feeder means the fish refuses to eat dead prey fish. In total, five SNPs were identified in genes. The effective allele numbers ranged from 1.1959 to 1.7001, with a mean of 1.4274 alleles per locus. The observed () values ranged from 0.1800 to 0.3585, and from 0.1655 to 0.4160, respectively. The value of polymorphism information content (PIC) was 0.2477, which is a classification of the median polymorphism level in the mandarin fish population. These results showed that the two genotypes TT and CT in the -A T/C of the SNP locus were significantly correlated with the high level of the food habit domestication traits in mandarin fish (<0.05). The three genotypes of genotype 1 (CT, CC/CT/TT, AA, AA, TT), genotype 2 (TT, CC/CT/TT, AA, AA, TT) and genotype 3 (TT, CC, AA, AA, TT) were also significantly associated with high levels of food habit domestication traits (<0.05). These genotypes affect the food habit domestication traits in mandarin fish, and genotype 2 had the highest correlation, which can be selected as the optimal genotype among individuals. In conclusion, our results demonstrated that these effective SNP molecular markers in genes could influence food habit traits in domestication of mandarin fish and could be used for accelerating the molecular marker-assisted selective breeding in mandarin fish. Based on the study of the SNPs association analysis of candidate genes with food habit domestication traits in mandarin fish, our findings could provide theoretical foundation and methodology for selectively breeding mandarin fish with increased tolerance to dead prey fish or artificial diets.