The cosmopolitan genus Elatine (Elatinaceae) includes about 25 aquatic species of mostly diminutive aquatic plants, whose relationships have not been evaluated using a phylogenetic approach. The taxonomic study of this group has been complicated by the small stature of the plants, their minute reproductive structures, and their cosmopolitan distribution. Consequently, much uncertainty exists with respect to species delimitations, their geographical distributions, and interspecific relationships. To clarify the infrageneric classification of Elatine and to provide insights on interspecific relationships within the genus, we conducted a phylogenetic study of nearly all (24) of the currently recognized species using both morphological and molecular data. The tree topology obtained based on morphological data (including vegetative and reproductive characters) was less-resolved than the trees based on molecular data, derived from either nuclear (ITS) or two plastid regions (matK/trnK and rbcL). However, the tree topology obtained from combined morphological and molecular data was well resolved and placed the morphologically distinctive E. alsinastrum as the sister group of the remaining species, which fell within two major clades: a clade of 4-merous-flowered species and a clade of 3-merous species, within which was embedded a subclade of 2-merous species. Although a number of topological differences occurred between the ITS and plastid tree topologies, significant incongruence was observed only for the placements of E. americana and E. hexandra, possibly resulting from reticulate evolution. Bergia, the sister genus of Elatine, comprises larger species, which often are mostly helophytic but never truly aquatic. Ancestral state reconstructions based on the ITS tree indicated that a morphological reduction series (in stature and floral merosity) exists among Elatine species, which is best explained as a consequence of adaptation to their aquatic life. These phylogenetic analyses also have helped to clarify the infrageneric classification of the genus and to provide a better understanding of the natural and nonindigenous distributions of the species. The new monotypic section Elatine sect. Cymifera, including E. brochonii, is described.