Abstract: PCR-SSCP and DNA sequencing was employed to analyze polymorphisms of the mitochondrial coding gene including ND1-6, ND4L, COX 1-3, ATP6 and ATP8 in Chinese Beijing duck and analyze their effects on carcass traits in Beijing duck. The results showed that 4 SNPs (G9259A, T9269C, G9394A and A9601G) were detected in ATP6 gene and 1 SNP (G9902A) was detected in COX 3 gene. The G9902A locus was a nonsynonymous which result in the varation of the coding amino acid (Arg56Gln). The COX 3 locus showed three genotypes (c. 9902GG, c. 9902GA and c. 9902AA) and the frequencies were 0.12, 0.23 and 0.6+5, respectively. The COX 3 locus was significantly associated with carcass traits of Beijing duck (p<0.05).