Background : Compositae is one of the largest plant families which has high probability of diversity and mutation. Though the various researches about the Compositae are ongoing, it is incomplete and need to be conducted the molecular genetic researches to back up the previous studies. This research was performed to identify the genetic divergence of Compositae plants based on the DNA barcoding for cpDNA-matK and rbcL regions. Methods and Results : For this studies, the genetic sequence analysis (SNP/InDel) and phylogenetic analysis were conducted by using Neighbor-Joining algorithm as targeting the nineteen specimens from 7 species which received a IT number along with NCBI Genbank database (http://ncbi.nlm.nih.gov) sequences. The result of matK sequence analysis, 68 SNP and 2 InDel regions (at nt 527-538bp and 695-706bp positions) were confirmed. Also 10 SNPs were found in rbcL region. The genetic divergence showed 0.000-0.059% in matK regions, and the mean was 0.024%. The highest distance were observed between Ligualria fischeri and the group composed with Aster tataricus and Solidago virgauria (2 and 3). The sequence divergence for rbcL regions showed 0.000-0.018%, and the mean was 0.005%. The highest sequence distance in rbcL region were observed between L. fischeri group and S. virgauria (HE574593). In result of phylogenetic analysis in matK region, the most species formed independent clade. A. tataricus in Aster genus and two samples of S. virguaria in Solidago genus were formed one same clade. S. virguaria(1) and A. spathulifolius(2) has been separated into independently for the plants belonging to same genus, respectively. A. spathulifolius showed differences with NCBI data. The rbcL formed one same clade except L. fischeri and Synurus deltoides. Conclusion : This study indicates that matK is more valuable than rbcL for the distinction among the species of Compositae. This results are expected to be used for the establishment of the classification system of Compositae as well as for the studies in the development of an authentication marker.