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<i>Knorringia sibirica</i> is a typical species of Polygonaceae with high medicinal and ecological value. However, there are few available phylogenetic and genetic studies about the chloroplast genome of <i>K. sibirica</i>. In the current study, a comprehensive examination of the chloroplast genome of <i>K. sibirica</i> was performed. The <i>K. sibirica</i> chloroplast genome is 161,384 bp, circular with a typical quadripartite structure, and comprised of guanine + cytosine content of 37.63%. The genome consists of 131 genes, including 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Seventy simple sequence repeats were identified in the genome. When compared with three closely related species, the result revealed that the chloroplast genome of <i>K. sibirica</i> was conserved in genome composition and structure. The specific sites in the genome suitable for DNA barcodes were identified by calculation of the nucleotide diversity. Finally, a phylogenetic tree of 49 species in Polygonaceae was constructed using the whole chloroplast genome. The phylogenetic analysis suggested that <i>Knorringia</i> is an independent genus in the Polygonea tribe. This research could provide support for the utilization of genetic sources and the evolutionary study of <i>K. sibirica</i>.