Abstract: The PCR technique was used to clone the Cytochrome b gene in thirteen individuals of Cherry Valley Duck breed. The genetic distances of thirteen sequences from Cherry Valley Duck were calculated based on the Kimura 2-parameter model, The overall average is 0.004, eighteen singleton variable sites were detected, 3 parsimony informative sites included. Two haplotypes were identified based on the three parsimony informative sites，with other eight duck breeds were selected from GenBank to construct phylogenetic tree, the Cherry Valley Duck and Anas superciliosa rogersi, Anas melleri, Anas luzonica, Anas undulate were ascribed into one group，The three parsimony informative sites can also classified the duck group into five haplotypes, the conclusions of our study can be used to screen genetical marker and analysis of duck group on genetic diversity.