Abstract: Rhei Radix et Rhizoma is one of the most used medicinal materials in China. Its original species are Rheum palmatum, Rh. tanguticum, and Rh. officinale. Rhei Radix et Rhizoma derived from different original species are significantly different in their active ingredients and pharmacological effects. To develop an accurate, rapid, and specific identification method, we obtained the chloroplast genomes of the three original species by Illumina Novaseq sequencing. We designed specific DNA barcodes from the hypervariable regions, which can accurately identify the three original species. The experimental results showed that the total length of the chloroplast genomes of Rh. tanguticum, Rh. officinale and Rh. palmatum were 161 039 bp, 161 093 bp, and 161 136 bp, respectively. All the three genomes were represented as typical quadripartite structures. A total of 131 genes, including 86 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes were identified from each chloroplast genome. Five pairs of primers based on the hypervariable regions were designed to efficiently amplify 42 samples. Results confirmed that five hypervariable regions, rps16-trnQ, psaA-ycf3, psbE-petL, ndhF-rpl32, and trnT-trnL, can be used as specific DNA barcodes for the identification of Rh. tanguticum, Rh. officinale, and Rh. palmatum. These results provided genetic information for further species identification of Rhei Radix et Rhizoma, and improve the safety of this clinical medication as well as standardize the market for Rhei Radix et Rhizoma.