Traditional Chinese medicine (TCM) plays an important role in the global traditional health systems. However, adulterated and counterfeit TCM is on the rise. DNA barcoding is an effective, rapid, and accurate technique for identifying plant species. In this study, we collected manuscripts on DNA barcoding published in the last decade and summarized the use of this technique in identifying 50 common Chinese herbs listed in the Chinese pharmacopoeia. Based on the dataset of the major seven DNA barcodes of plants in the NCBI database, the strengths and limitations of the barcodes and their derivative barcoding technology, including single-locus barcode, multi-locus barcoding, super-barcoding, meta-barcoding, and mini-barcoding, were illustrated. In addition, the advances in DNA barcoding, particularly identifying plant species for TCM using machine learning technology, are also reviewed. Finally, the selection process of an ideal DNA barcoding technique for accurate identification of a given TCM plant species was also outlined.

AquilariaLam. is an important group of trees that produce agarwood, which is widely used for manufacturing medicine, perfumes and incense. The members of the genusAquilariaare close to being extinct due to illegal harvesting and are now protected in many countries. In this study, five DNA barcodes [internal transcribed spacer (ITS), maturase K (matK),psbA-trnH, ribulose bisphosphate carboxylase (rbcL) andtrnL-trnF] and their combinations were evaluated for the discrimination of the major (16 out of 21) species ofAquilariabased on three criteria: sequence variation, genetic distances and the discrimination ability. In addition, we attempted to determine the phylogenetic relationship betweenAquilariaandGyrinopsspecies using three phylogenetic analysis methods. We observed that the combination barcode ITS+trnL-trnF had a good discrimination ability based on the best match and best close match methods, provided more genetic information, and clearly indicated the comprehensive phylogenetic relationship between mostAquilariaandGyrinopsspecies. Considering the overall performance of these barcodes, the ITS+trnL-trnF is a suitable barcode for the identification ofAquilariaspecies.

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