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Cirsium japonicum (C. japonicum) is an important oriental herb belonging to the family Asteraceae. The C. japonicum complete chloroplast genome is composed of 152,606 bp, which form a large single-copy region (LSC, 83,492 bp), a small single-copy region (SSC, 18,772 bp), and 2 inverted repeats (IRs, 25,196 bp). There are 114 genes annotated, including 80 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. Our phylogenetic analysis suggests that C. japonicum is closely related to the Cirsium genus of the Asteraceae family, and that C. japonicum (subfamily: Carduoideae) is separate from the Asteroideae subfamily.