To evaluate the identification efficiencies of the DNA barcode sequences for the medicinal plants of Polygonatum. Methods: The chloroplast psbA-trnH, matK, and rbcL and nuclear ITS and ITS2 of 44 Polygonatum samples were amplified using the universal primers. The intra-and inter-specific genetic distance and barcoding gap were analyzed. The identification efficiencies of the sequences were calculated by BLAST and Nearest Distance methods. Results: ITS and ITS2 of Polygonatum were difficult to obtain using the universal primers. The available rbcL were the highest while the psbA-trnH was the lowest. The intra-and inter-specific genetic distances were all low and no obvious barcode gap existed in three candidate loci. The identification efficiencies of the three chloroplast regions were all low according to BLAST and Nearest Distance methods. Conclusion: The DNA barcode sequences did not meet the demands of identifying the medicinal plants of Polygonatum, and the complete chloroplast genome sequences(CP)or the suitable regions screened from CP may be applied to identify the medicinal plants of Polygonatum in the future.