The study reports that the mitochondrial genome of F. multiflora comprises two circular chromosomes measuring 200,352 and 112,098 nucleotides, respectively. These chromosomes collectively encode 57 genes, including 34 protein-coding genes, 20 transfer RNA genes, and three ribosomal RNA genes. Phylogenetic analysis indicates that F. multiflora is closely related to Beta macrocarpa and Silene latifolia. The article discusses the potential benefits of the findings. Understanding the multipartite structure of the Fallopia multiflora mitochondrial genome provides valuable insights into the plant’s evolutionary history, genetic diversity, and adaptation mechanisms. These findings can aid in further research on the plant’s metabolic pathways, particularly those related to its medicinal properties, and may contribute to improved breeding strategies and conservation efforts. Additionally, genetic insights may enhance the understanding of how mitochondrial functions influence the production of bioactive compounds, which are responsible for Fo-TI’s reputed health benefits.