In order to analyze the association between mitochondrial protein-coding genes and body color traits of black carp (Mylopharyngodon piceus) and screen out SNP markers related to body color, this study selected the skin tissues of five Foshan gray black carp samples and five Hanjiang black M. piceus samples and detected the relative expression of 13 mitochondrial protein-coding genes in the skin tissues of the two color populations by qPCR, and then performed the significance analysis. The study designed primers for the CDS region sequence of the protein-coding gene with the most obvious expression difference, and then selected 78 Foshan gray M. piceus samples and 92 Hanjiang black M. piceus samples for sequencing, and screened out SNP markers based on the sequencing peak map. The results showed that among the 13 mitochondrial protein coding genes, the relative expression of ND4L gene is the most significant, the relative expression of COⅡ gene is the highest, and the relative expression of ND5 gene is the lowest. Two SNPS (C252T and A243G) were detected in the mitochondrial ND4L gene of 170 M. piceus samples. The frequencies of A and G genotypes at A243G in Foshan gray body color population are 96.2% and 3.8%, while the frequencies of T and C genotypes at C252T are 38.5% and 61.5%. The frequencies of A and G genotypes of C252T locus in Han Jiang normal body color population are 100% and 0%, while the frequencies of T and C genotypes of C252T locus are 15.2% and 84.8%. Three haplotypes, AC, AT and GC were detected. AC shows the highest frequency; AC and AT are distributed in both body colors, while GC shows the lowest frequency and only appeares in normal body colors. This study studied the distribution of genotypes and haplotypes of two SNPS in mitochondrial ND4L gene related to body color of M. piceus and provided theoretical guidance for the study of body color and growth traits of M. piceus as well as the breeding of M. piceus.