New World Podostemaceae (riverweeds) comprise approximately 135 species in 21 genera, most of which are of tropical distribution, shed pollen in monads, and belong to subfamily Podostemoideae. We undertook a phylogenetic study of Neotropical Podostemoideae using molecular (ITS, rbcL, trnL) and morphological data, to assess the monophyly of genera and their interrelationships. Extensive taxon sampling (38 taxa in 15 genera) revealed that the large genera Apinagia and Marathrum are not monophyletic as currently circumscribed, although several species of the former comprised a clade that could be delimited morphologically by the shared character of upright stems (i.e. anchored to the substrate only basally). Marathrum species were split geographically, with Central and South American taxa resolving in different clades. Oserya also comprised two geographically disparate clades, with the type species belonging to the South American clade. To establish the monophyly of Oserya, we erected a new genus Noveloa to accommodate the Central American species N. coulteriana and N. longifolia. The Central American Marathrum clade included the monotypic Vanroyenella, which we transferred to that genus as Marathrum plumosum. The genera Castelnavia and Rhyncholacis were monophyletic in our analyses; C. multipartita f. pendulosa was elevated to species rank as Castelnavia pendulosa. The monotypic Lonchostephus resolved within Mourera, with which it shares a number of morphological features that are found also in Tulasneantha (also monotypic), but which otherwise are unique in Podostemaceae. We recommend that Lonchostephus and Tulasneantha be merged with Mourera and provide the new combination Mourera monadelpha for the latter. Finally, an unexpected clade of morphologically diverse genera, including members of Apinagia, Jenmaniella, Lophogyne, Marathrum, and Monostylis, resolved with strong support but uncertain morphological integrity, as sister to all ingroup taxa except Mourera. However, nomenclatural changes in this group have not been made, pending additional taxon sampling and procurement of further molecular and morphological evidence.