Alismataceae is one of the early diverged families of monocotyledonous plants. We report the complete chloroplast genomes of three species, including (Sam.) Juzep. 1934, Raf. 1908, and Pursh 1813, of which is a traditional Chinese medical plant used widely to treat diuretics, diabetes, hepatitis, and inflammation. We sequenced the complete chloroplast genomes with the Illumina Nova-Seq 6000 platform using herbarium collections. The chloroplast genomes of , and are 159,861 bp, 160,180 bp, and 159,727 bp in length, respectively. The three chloroplast genomes each contain 113 genes, including four rRNAs, 30 tRNAs genes, and 79 protein-coding genes, and the average GC content is 36.0%. Based on the whole chloroplast genomes of 19 species of Alismataceae and the close allies, the medicinally important was found to be closely related to another medicinal plant L. 1753 in the phylogenetic analysis. The genus was supported to be monophyletic.