A comparative analysis of chloroplast genomes revealed the chloroplast heteroplasmy of .

L. is the main source of artemisinin, an antimalarial drug. High diversity of morphological characteristics and artemisinin contents of has affected the stable production of artemisinin while efficient discrimination method of strains is not available. The complete chloroplast (cp) genomes of 38 strains were assembled and analyzed in this study. Phylogenetic analysis of species showed that distinct intraspecific divergence occurred in strains. A total of 38 strains were divided into two distinct lineages, one lineage containing widely-distributed strains and the other lineage only containing strains from northern China. The cp genomes ranged from 150, 953 to 150, 974 bp and contained 131 genes, and no presence or absence variation of genes was observed. The IRs and SC junctions were located in 19 and 1, respectively, without IR contraction observed. Rich sequence polymorphisms were observed among strains, and a total of 60 polymorphic sites representing 14 haplotypes were identified which unfolding the cpDNA heteroplasmy of . In conclusion, this study provided valuable resource for strains identification and provided new insights into the evolutionary characteristics of .