OBJECTIVE To identify Ginseng Flos and their confounds by using the high-throughput sequencing technology, and to verify the accuracy of high-throughput sequencing technology in species identification by using ITS2 sequencing technology. METHODS High-throughput sequencing was performed on the amplified products of Ginseng Flos adulterated samples, use cutadapt, PEAR, PRINSEQ, Usearch, RDP classifier, SINTAX software to obtain operational taxonomic unit(OUT) sequences, remove fungi, unclassified and other non-green plant sequences. To avoid false positives, delete OTU sequences with a sequence number <100 or base numbers <200 bp. The ITS2 amplification products of Ginseng Flos, Quinquefolii Flos, and Notoginseng Flos were sequenced. To verify the accuracy of high-throughput sequencing technology for species identification, MEGA 11.0 was used to construct neighbor joining system cluster tree, genetic distance, interspecific information loci and Blast analysis of ITS2 and OTU base sequences of Ginseng Flos, Quinquefolii Flos, and Notoginseng Flos. RESULTS A total of 54 653 valid sequences were obtained by high-throughput sequencing, the serial numbers of Ginseng Flos, Quinquefolii Flos, and Notoginseng Flos were OTU1, OTU2, OTU3, respectively, and the corresponding effective sequences were 31 325, 857 and 442, respectively. By performing a Blast search of ITS2 and OTU base sequences of each species, each species was supported. The genetic distance between Ginseng Flos and Quinquefolii Flos and Notoginseng Flos was 0.010 and 0.033, respectively. Ginseng Flos and Quinquefolii Flos, Notoginseng Flos had 2 and 7 information sites, respectively. The neighbor join system cluster tree showed that the species were clustered independently into one branch, with Ginseng Flos, and Quinquefolii Flos clustered as a large branch and juxtaposed with Notoginseng Flos. Ginseng Flos was the same as Quinquefolii Flos secondary structure, but with Notoginseng Flos there were three different positions but there were A, B and C differences between arm Ⅳ and arm Ⅰ of Notoginseng Flos. CONCLUSION The high-throughput sequencing technology can accurately identify Ginseng Flos, Quinquefolii Flos and Notoginseng Flos, and has a strong ability to identify adulterated samples, which provides a certain idea for the identification of commercial Ginseng Flos.