plants are widely distributed across Asia and Europe, yet their intricate phylogenetic relationships pose significant challenges for systematic studies and interspecies identification. : To clarify the mitochondrial and chloroplast genomes of var. , and to reveal its evolutionary relationship and historical gene flow with domesticated cherries. : In this study, we assembled, annotated, and analyzed the first mitochondrial and chloroplast genomes of var. , a species within the genus. : The mitochondrial genome was found to be 484,858 base pairs in length, exhibiting a typical circular conformation. Phylogenetic analysis revealed a close evolutionary relationship between and , suggesting historical gene flow between these two species last genomes; mitochondrial genomes; phylogeny analysis. : To provide a genomic basis for resolving the phylogenetic controversies within the Li-associated plants, elucidating their evolutionary mechanisms, and formulating breeding strategies.