Amomum contains 150 species, and 39 of them are found in China. Many Amomum species are used in traditional Chinese medicines and favorite food condiment. The intrageneric classification of this genus is largely unclear, and the accurate identification of species is difficult. DNA barcoding is a technique to identify species using standardized DNA region. The COI sequence has been successfully used to identify animal species. Unfortunately, there are no universally accepted barcode systems for plants. This study compared the each three candidate plastid regions (matK, rbcLa, trnHpsbA) and the combined data (matK+rbcLa, matK+trnHpsbA, rbcLa+trnHpsbA, matK+rbcLa+trnHpsbA) among 121 accessions representing 50 species of the genus. In order to screen out the suitable barcode for identifying the species of Amomum, Taxon DNA was used to estimate the barcoding gap between interspecific and intraspecific distances, and BLASTn was used to calculate the rate of correct identification. The results indicated that there was no DNA barcode gap in three loci. The correct identification of matK was higher than that of trnHpsbA or rbcLa, the combined data has higher correct identification than that of single one, and the threelocus combined data showed the greatest level of species discrimination. To sum up, matK+rbcLa+trnHpsbA can be considered as a potential barcode for identifying the species of Amomum.