| Summary: | <i>Reynoutria japonica</i> Houtt., a traditional medicine herb of the Polygonaceae family, has been used since ancient times in China due to its various pharmacological effects. Chloroplast genomes are conservative and play an essential role in population diversity analysis. However, there are few studies on the chloroplast genome of <i>R</i><i>. japonica</i>. In this study, the complete chloroplast genomes of three <i>R. japonica</i> from different regions were performed by next-generation sequencing technology. The results revealed that the lengths of the three chloroplast genomes are between 163,371~163,372 bp, and they have a highly conserved structure with a pair of inverted repeat (IR) regions (31,121 bp), a large single-copy (LSC) region (87,571~87,572 bp), and a small single-copy (SSC) region (13,558 bp). In total, 132 genes were annotated, including 8 rRNA genes, 37 tRNA genes, and 87 protein-coding genes. The phylogenetic analysis strongly revealed that 13 populations of <i>R. japonica</i> form a monophyly, and <i>Fallopia multiflora</i> (Polygonaceae) is its closest species. The two species diverged at ~20.47 million years ago, and <i>R. japonica</i> in China could be further divided into two major groups based on genetic structure analysis. In addition, several potential loci with suitable polymorphism were identified as molecular markers. Our study provides important genetic resources for further development and utilization of <i>R. japonica</i> germplasm, as well as some new insights into the evolutionary characteristics of this medicinal plant.
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