The study was conducted to compare the diversity of three sequences of DNA barcodes (atpF-atpH spacer, ITS region, and rbcL gene) of Elephantopus mollis H.B.K. and Elephantopus scaber L.. Three individuals were represented for each species and were collected at an indigenous location in Bay Nui area, An Giang province, Vietnam. The results showed that DNA barcodes were successfully amplified. The ITS and rbcL regions had no difference in the nucleotide sequences of samples in each species, except that atpF-atpH region had a difference at the 37th nucleotide position of E. mollis H.B.K. The results of sequence polymorphism analysis showed that the ITS region had higher variation than the two regions of atpF-atpH and rbcL through the percent identity of 89.58, 98.99 and 100%, respectively. The result of analyzing phylogenetic trees of DNA sequences through genetic distance and bootstrap values showed that the ITS region could genetically distinguish between E. mollis H.B.K. and E. scaber L. and from some other species higher than the other two regions.