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Background Hydrocharis  L. and  Limnobium  Rich. are small aquatic genera, including three and two species, respectively. The taxonomic status, phylogenetic relationships and biogeographical history of these genera have remained unclear, owing to the lack of Central African endemic  H. chevalieri  from all previous studies. We sequenced and assembled plastomes of all three  Hydrocharis  species and  Limnobium laevigatum  to explore the phylogenetic and biogeographical history of these aquatic plants. Results All four newly generated plastomes were conserved in genome structure, gene content, and gene order. However, they differed in size, the number of repeat sequences, and inverted repeat borders. Our phylogenomic analyses recovered non-monophyletic  Hydrocharis . The African species  H. chevalieri  was fully supported as sister to the rest of the species, and  L. laevigatum  was nested in  Hydrocharis  as a sister to  H .  dubia .  Hydrocharis-Limnobium  initially diverged from the remaining genera at ca. 53.3 Ma, then began to diversify at ca. 30.9 Ma. The biogeographic analysis suggested that  Hydrocharis  probably originated in Europe and Central Africa. Conclusion Based on the phylogenetic results, morphological similarity and small size of the genera, the most reasonable taxonomic solution to the non-monophyly of  Hydrocharis  is to treat  Limnobium  as its synonym. The African endemic  H. chevalieri  is fully supported as a sister to the remaining species.  Hydrocharis  mainly diversified in the Miocene, during which rapid climate change may have contributed to the speciation and extinctions. The American species of former  Limnobium  probably dispersed to America through the Bering Land Bridge during the Miocene.

Plastome phylogenomics and historical biogeography of aquatic plant genus Hydrocharis (Hydrocharitaceae)