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Ephedrae Herba and Ephedrae Radix et Rhizoma (Mahuang) have been used as Chinese herbal medicines.  Ephedra  plants mainly live in deserts and have good governance of desertification. Despite their important medicinal and environmental protection value, dietary supplements containing ephedrine from  Ephedra  species may threaten the health of people. Morphological resemblance amongst species causes difficulty in identifying the original species of  Ephedra  herbs. Chloroplast (CP) genome shows good prospects in identification and phylogenetic analysis. This study introduced the structures of the CP genomes of three  Ephedra  species and analysed their phylogenetic relationships. Three complete CP genomes of  Ephedra  showed four-part annular structures, namely, two single-copy regions and two inverted repeat regions. The entire CP genomes of three  Ephedra  species in terms of size were 109,550 bp ( E. sinica ), 109,667 bp ( E. intermedia ), and 109,558 bp ( E. equisetina ). Each CP genome of the three  Ephedra  species encoded 118 genes, including 73 protein-coding genes, 37 tRNA genes and 8 ribosomal RNA genes. Eleven high-variation regions were screened through mVISTA to be potential specific DNA barcodes for identifying  Ephedra  species. Maximum likelihood and maximum parsimony trees showed that CP genomes could be used to identify  Ephedra  species. The  Ephedra  species had a close phylogenetic relationship with  Gnetum  species and  Welwitschia mirabilis . This research provided valuable information for the identification and phylogenetic analysis of gymnosperms and drug safety of  Ephedra .

Identification and Phylogenetic Analysis of the Complete Chloroplast Genomes of Three Ephedra Herbs Containing Ephedrine