Aquatic plants, and especially the emblematic genus Baldellia (Alismataceae), are among the most threatened organisms, due to unprecedented human-driven habitat destructions. Therefore protection plans are crucially needed and call for thoroughly documenting the genetic diversity and clarifying the taxonomy of this endangered genus. Our sampling included 282 individuals from 42 natural populations and covered the whole geographical range of the genus, across Europe and the Mediterranean. We combined sequencing of nuclear internal transcribed spacer (ITS) and chloroplastic trnL-ndhF regions with amplified fragment length polymorphism (AFLP) genotyping to investigate the Alismataceae phylogeny, and produce a phylogeography of Baldellia. Our phylogeny strongly supported the monophyly of Baldellia and placed it as the sister clade to Luronium and Alisma, therefore excluding, as previously supposed, a close genetic relatedness to the predominantly neotropical genus Echinodorus. The phylogeography of Baldellia outlined patterns consistent with a hypothesis considering glacial refugia located in the Iberian Peninsula and the Italy/Balkan region from which two distinct genetic lineages re-colonized Europe. These two lineages corresponded respectively to Baldellia ranunculoides (Italy/Balkan derived populations) and Baldellia repens (populations recovered from the Iberian Peninsula refuge), therefore supporting differences outlined between the two taxa in previous ecological and morphological studies. These results allowed clarifying taxonomic uncertainties by confirming the genetic distinctness of B. repens according to B. ranunculoides. A third lineage, Baldellia alpestris, originated and remained endemic to the mountainous regions of the Iberian Peninsula. Unexpectedly, B. repens populations collected in northern Africa, appeared to be genetically distinct from their European counterparts, this calls for further investigation to fully address their genetic and conservation status. Finally, we detected a large hybridization zone in northwestern Europe between B. repens and B. ranunculoides. These results were discussed in light of conservation approaches for Baldellia populations.