A total evidence phylogeny for Pontederiaceae is herein presented based on new morphological and previously published molecular data. Our results led us to re-circumscribe Pontederia to include Monochoria, Pontederia s.s. and the polyphyletic Eichhornia. We provide the needed ten new combinations and 16 typifications, arrange a total of 25 accepted species (six representing re-established names) in 5 new subgenera. Furthermore, we provide an identification key for the two genera accepted by us in Pontederiaceae, an identification key to the subgenera, identification keys to the species of each subgenus and commentaries on Pontederia s.l., as well as for each subgenus and each species.