The plant family chrysanthemum is known for its medicinal, ornamental, and economic purposes. Owing to its economic and biological significance to the difficult identification based on morphological characters, it is useful to develop DNA barcodes. DNA sequence data enable not only the inference of phylogenetic relationships but also provide an efficient method for species-level identifications under terms DNA barcoding or DNA taxonomy. The purpose of this study is to evaluate the utility of DNA barcoding in discriminating Chrysanthemum species. Four cpDNA regions (matK, rpoC, rpoB, trnH-psbA) and one nuclear (ITS) marker have sequenced from 28 specimens of 11 species from 4 genera of Chrysanthemum which were collected from 5 provinces in Korea. Comparisons of within and between species levels of sequence divergence showed that genetic variation between species exceeds variation within species.