Persicaria amphibia (L.) Delarbre, also known as water knotweed, belongs to the Polygonaceae family and has two types: terrestrial and aquatic. We report the chloroplast genome of P. amphibia obtained through de novo assembly of Illumina paired-end reads produced by total DNA sequencing. We analyzed the complete chloroplast (cp) genome of P. amphibia and found it to be 159,455 bp in length, with a large single-copy region (LSC, 84,281 bp), a small single-copy region (SSC, 13,258 bp), and a pair of inverted repeats (IR, 30,956 bp). It contains 79 protein-coding, 29 tRNA and 4 rRNA genes. Comparative analysis of nine Persicaria cp genomes showed a similar genome structure and gene content. However, ycf3 intron II was lost in three Persicaria species (P. hydropiper, P. japonica, and P. pubescens) and the SC/IR regions of four species (P. amphibia, P. hydropiper, P. japonica, and P. pubescens) included the rps19 gene. Phylogenetic analysis of the nine Persicaria species revealed that P. amphibia is sister to P. hydropiper, P. japonica, and P. pubescens. Moreover, we found sequence divergence regions; the largest were rps16-trnQ, trnQ-psbK, trnW-trnP, ndhF-rpl32, and rpl32-trnL regions. This study could be useful for phylogenetic tree analysis of Persicaria and for the identification of Persicaria species.