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We reported the complete chloroplast genome sequence of Rumex japonicus in Dok-do Island, Korea. The genome size was 159,223 bp in total length with one large single-copy (LSC; 84,962 bp), one small single-copy (SSC; 12,999 bp), and 2 inverted repeat (IR) regions (IRa and IRb, each with 30,631 bp). The overall GC content was 37.5% and the genome contained 131 genes, including 83 protein-coding, 38 transfer RNA and 8 ribosomal RNA genes. Phylogenetic analysis supported monophyly of subgenus Rumex and determined the phylogenetic position of R. japonicus as sister to the clade containing R. crispus and R. nepalensis.