Monochoria is a pantropical genus of aquatic plants belonging to the family Pontederiaceae (Commelinales) with many narrowly distributed taxa in Africa and Asia-Pacific. Various key taxonomic questions remain unaddressed in the latter region, especially with regards to apparent cryptic diversity within M. hastata and M.vaginalis, two widespread species complexes. Here we test taxonomic concepts and evaluate species boundaries using a phylogenetic framework. We collected virtually all species of Monochoria, apart from a small number of extremely rare species of Africa and Australia, ensuring that multiple samples of M.hastata and M. vaginalis were obtained throughout their ranges, from Myanmar to Indonesia and from India to Japan, respectively, to enable an appraisal of species boundaries and intraspecific variation. Molecular phylogenetic trees based on five plastid DNA markers and the nuclear TOPO6 region shared almost identical topologies. Species delimitation analyses using the well-sampled plastid DNA data set discerned eleven to twelve species. The results lead us to conclude that certain populations in the Asia-Pacific region represent hitherto unrecognised or overlooked cryptic taxa within widespread species complexes. One new species, M. pseudohastata, is described and one synonym is resurrected.