Abstract: In order to analyze the distribution pattern and biogeographic evolution in genetic diversity of domestic ducks of this marker, the mitochondrial D-loop of 106 samples collected from 9 breeds of domestic ducks were sequenced, and 31 haplotypes were identified. The results showed the genetic diversity of mitochondrial DNA in breeds at middle reaches of Changjiang River was bigger than that at the lower reaches of Changjiang River. A unconspicuous negative correlation was observed between the estimated level of gene flow(Nm) and the geographic distance among breeds. The mismatch distribution of the haplotypes and neutrality tests of the Tajima’s D both showed that there might not be a population expansion and the population size was steady. Phylogenetic tree analysis demonstrated that no geographic clustering was observed, haplotypes were shared among geographic populations and an interwoven distribution pattern was presented.