In this study, we report the complete plastome sequence of <i>Cardamine glechomifolia</i> H.Lév. 1913 (NCBI acc. no. OP894664). This plastome shows typical quadripartite structure. The plastome size is 154,307 bp, which consists of 84,015 bp large single-copy (LSC), 17,690 bp small single-copy (SSC), and 26,301 bp inverted repeat (IR) regions. The plastome contains 112 genes, including 78 protein-coding, 30 tRNA, and four rRNA genes. The <i>inf</i>A gene is pseudogenized. Sixteen genes contain one intron and two genes (<i>clp</i>P and <i>ycf</i>3) have two introns. The phylogenomic analysis conducted in our study reveals that the genus <i>Cardamine</i>, which encompasses <i>C. glechomifolia</i>, exhibits three distinct clades. In order to elucidate the interrelationship among the three clades, it is imperative to conduct additional investigations by augmenting the number of <i>Cardamine</i> samples.