To investigate the population structure and systematic evolution of the domestic duck in China, we sequenced the 667 bp mitochondrial DNA (mtDNA) D-loop control region of 106 ducks from nine breeds along the Yangtze-Huai River. Of the total analyzed sites, 34 (5.1%) were polymorphic due to transitions, transversions, insertions, and deletions. Nucleotide content was 25.6% A, 33.3% C, 15.2% G, and 25.9% T. In total, 31 haplotypes were identified in the target region; of these, the major haplotype was A7, and nine haplotypes were shared by the tested ducks. The haplotype diversity (Hd) and average nucleotide diversity (Pi) were 0.798% and 0.28%, respectively. Hd was highest in the Jingjiang shelduck, followed by the Youxian and Enshi shelducks, and it was lowest in the Wendeng black duck. Nucleotide diversity (Dxy) among the nine breeds ranged from 0.139 to 0.433%, and the Kimura 2-parameter distances were 0.0013-0.0044. Molecular variance indicated that a very high proportion of the insignificant genetic variance was attributable to variations within breeds. Phylogenetic analysis of 31 haplotypes revealed only one distinct maternal lineage in the tested ducks, and no evidence was found of a contribution of the Anas zonorhyncha group B haplotype to the maternal origin of Chinese domestic duck breeds along the Yangtze-Huai.