The cosmopolitan genus Nymphoides contains approximately 50 species that vary considerably in growth habit, inflorescence architecture, and in vegetative, floral, and seed morphology We undertook a phylogenetic study of 31 Nymphoides species, including all species native to Australia, to evaluate interspecific relationships and to infer the evolution of heterostyly and inflorescence architecture. Phylogenetic analysis of morphological data resolved several clades of species, but with poor branch support. Molecular data from nuclear (ITS) and plastid (matK/trnK) DNA sequences were significantly incongruent regarding the phylogenetic placement of many clades and species. Two major clades were resolved consistently: a clade sister to N. minima and the clade comprising these two lineages. Incongruent phylogenetic placements of several Nymphoides species were attributed to putative ancestral hybridization that produced conflicting phylogenetic signals between the maternally inherited cpDNA and the biparentally inherited nuclear DNA (subsequently homogenized to a single allelic variant by concerted evolution). Ancestral character state reconstruction indicated that the first Nymphoides species were heterostylous, followed by four independent transitions to homostyly and up to four subsequent reversions back to heterostyly. The evolutionary history of dioecy and gynodioecy could not be ascertained with confidence, owing to incomplete taxon sampling, poor resolution of crown clades, and incongruence between nuclear and plastid sequence data. Ancestral state reconstruction also indicated that the expanded inflorescence morphology found in several Australian and tropical Asian Nymphoides species represents the ancestral condition for the genus, from which a condensed morphology (found in most other Nymphoides species worldwide) evolved independently at least twice.