Maintaining native species are very important for the conservation of genetic resources in the world. In order to investigate relationships of the wild and domestic duck species, 55 ducks from ten breeds were sampled from nine different geographical areas in Korea. Of these, 27 samples are represented as Mallad (Anas platyrhynchos), Spot-billed (Anas poecilorhyncha) and domestic (Anas platyrhynchos domesticus) ducks. The partial (746 and 749 bp) mitochondrial DNA (mtDNA) D-loop region sequences were obtained and 216 SNPs were identified, which belong to 68 haplotypes. Based on the neighbor-joining (NJ) method, duck species used in this study can be well differentiated, except for the three duck breeds, Mallard, Spot-billed and domestic ducks, where most of the individuals belong to haplotype 39. Based on our results, duck species can be discriminated well with mtDNA sequences, except for the three closely related breeds, and this can be effectively used for an appropriate conservation program for the wild duck species in Korea.