Abstract：In this research DNA Barcodes was based on the special section of the cytochrome c oxidase 1 (COⅠ)sequence. Three primers were designed in three special sections(Bar1 Bar2) to identify six indigenous chicken breeds. The Bar1 sequence of COⅠ(648 bp : from 712 sites to 1358 sites) was the highest in polymorphism and had 24 SNP in six chicken breeds. The average interspecific divergence was 3.860%, and special sites were found in each chicken breed which was the bases to identifying chicken breeds. The DNA taxonomy of Bar1 used NJ was consistent with morphological taxonomy among the six indigenous chicken breeds. However, the analysis of Bar2 sequences of COⅠindicated that they were lower polymorphism and no special site in most chicken breeds which was not benefit to identify chicken breeds. The DNA taxonomy of Bar2 used NJ was not consistent with morphological taxonomy among the six indigenous chicken breeds. The results illustrated that the DNA barcoding was a rapid and inexpensive method for the identifying breeds, especially when coupled with traditional taxonomic tools in disclosing hidden diversity and molecular phylogeny relationship. It was a better tool for identifying chicken breeds through more improvement.
