In order to evaluate the efficiency of ITS2 and psbA-trnH sequences used as DNA barcodes to distinguish Plantaginis Semen from its adulterants, we collected 71 samples of Plantaginis Semen and its adulterants. The ITS2 and psbA-trnH sequences were aligned through Clustal W, and the genetic distances were calculated by kimura 2-parameter (K2P) model and the Neighbor-Joining (NJ) phylogenetic trees were constructed using MEGA 5.1. The results indicated that the ITS2 sequence lengths of Plantago asiatica and P. depressa were 199 bp and 200 bp, respectively; the maximum intra-specific K2P distance were lower than the minimum inter-specific K2P distance; the NJ tree based on ITS2 sequence indicated that Plantaginis Semen and its adulterants could be distinguished clearly. The sequence lengths of psbA-trnH of both P. asiatica and P. depressa were 340 bp; the maximum intra-specific K2P distances were lower than the minimum inter-specific K2P distance; the NJ tree based on psbA-trnH sequence showed that Plantaginis Semen can be distinguished clearly from its adulterants except for P. major. Therefore, ITS2 sequences can be used as an ideal DNA barcode to distinguish Plantaginis Semen from its adulterants.