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The genus <i>Rorippa</i> belongs to the family Brassicaceae, and its members usually have high medicinal value. The genus consists of approximately 75 species and mainly grows in the Northern Hemisphere, occurring in every continent except Antarctica. The taxonomy and phylogenetic relationships of <i>Rorippa</i> are still unsettled, largely due to complex morphological variations in <i>Rorippa</i>, which were caused by frequent hybridization events. Here, we sequenced four complete plastid genomes of <i>Rorippa</i> species by Illumina paired-end sequencing. The four new plastid genomes of <i>Rorippa</i> ranged in total size from 154,671 bp for <i>R. palustris</i> to 154,894 bp for <i>R. sylvestris</i>. There are 130 genes in the four plastomes, embodying 8 rRNA, 37 tRNA, and 85 protein-coding genes. Combining with six published plastid genomes, we carried on comparative and phylogenetic analyses. We found that the ten <i>Rorippa</i> plastid genomes were conservative in gene number and order, total size, genomic structure, codon usage, long repeat sequence, and SSR. Fourteen mutational hotspot regions could be selected as candidate DNA barcoding to distinguish <i>Rorippa</i> plants. The phylogenetic trees clearly identified that ten <i>Rorippa</i> species displayed monophyletic relationships within the tribe Cardamineae based on plastomes and nrDNA ITS sequences. However, there are significant cytonuclear discordances in the interspecific relationships within <i>Rorippa</i>, as well as the intergeneric relationships between <i>Rorippa</i> and its related genera. We inferred that the cytonuclear discordance is most likely a result of interspecific hybridization within <i>Rorippa</i>, as well as intergeneric hybridization with its related genera. These plastid genomes can offer precious information for studies of species authentication, evolutionary history, and the phylogeny of <i>Rorippa</i>.