Elatine rotundifolia was described in 2008 from Ecuador as a new species because of its unique morphology and geographical distribution. However, an examination of type material for E. rotundifolia suggested to us initially that this taxon had been assigned incorrectly to Elatine, despite some superficial similarity to that genus. This possibility was investigated using morphological and molecular data. We found that E. rotundifolia differed from other members of Elatine by several vegetative and reproductive features, which indicated a distant alliance closer to Linderniaceae (Lamiids; Asterids) rather than Elatinaceae (Fabids; Superrosids). We then conducted a phylogenetic analysis of DNA sequences from the internal transcribed spacer region, which included isotype material of E. rotundifolia, as well as various representatives of Elatinaceae, Linderniaceae, and other angiosperm clades. The molecular data resolved E. rotundifolia among several accessions of Micranthemum (Linderniaceae) in a position quite remote phylogenetically from accessions of Bergia and Elatine (Elatinaceae). From these results, we conclude that the name E. rotundifolia refers to a taxon that was misplaced in Elatine, and represents instead a member of Micranthemum (Linderniaceae), and possibly is synonymous with the aquatic species M. umbrosum.