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Persicaria maackiana (Regel) Nakai ex T. Mori (1922), a species of the Polygonaceae family, is an annual plant widely distributed in Northeast Asia. We aimed to sequence the complete chloroplast genome of P. maackiana using Illumina HiSeq paired-end sequencing. The chloroplast genome was determined to be 160,635 bp. The complete chloroplast genome contained 129 genes, including 84 protein-coding genes, 37 tRNA, and eight rRNA genes. Phylogenetic analysis of the chloroplast genome sequences of 15 Polygonaceae plants revealed that P. maackiana was most closely related to P. perfoliata. Our findings might be useful for future phylogenetic studies of Polygonaceae.