Abstract: The PCR technique was used to analyze the mtDNA D-loop sequences in 20 individuals of five duck strains. The PCR products were purified and sequenced. As a result, a series of 710bp nucleotide sequences of partial D-loop region were obtained. Comparing the D-loop fragments with each other by Mega software,86 sites were variable among all the partial mitochondrial D-loop region sequences including 16 parsimonious message sites. The relative genetic distances were calculated among individuals by “Pairwise distance” method of Mega. The results indicated that the differentiation of the 20 sequences ranged from 0.000 to 0.082 and showed 18 kinds of haplotypes among 20 individuals and construct phylogenetic trees. The number of polymorphic sites (S) was 86;the nucleotide diversity（Pi）and the average number of nucleotide differences（K）were 0.01911 and 13.3588,respectively.It can be concluded that the variation in mtDNA D-loop region sequences of duck strains was less relatively. But the genetic diversity of duck strains was higher relatively. As a result, mtDNA D-loop region sequences can be used to scan genetic diversity of populations.