Plants that have adapted to grow as submersed aquatics are relatively rare among angiosperms, yet they represent a convergent strategy that has evolved in many groups. Asteraceae tribe Eupatorieae include a number of obligate wetland species, but only three genera (Gymnocoronis, Sclerolepis, and Shinnersia) routinely grow submersed. We conducted a molecular phylogenetic study of Eupatorieae to assess the relationships among aquatic genera and to infer the evolutionary history of the submersed aquatic habit. Two major clades were identified in Eupatorieae, corresponding to base chromosome numbers of x = 10 or fewer, and x = 11 or greater. We determined that submersed aquatics evolved independently in two subtribes, Adenostemmatinae (Gymnocoronis; x = 10) and Trichocoroninae (Sclerolepis and Shinnersia; x = 15), each belonging to a separate major clade, and that the aquatic lineages evolved in allopatry. Sparse taxon sampling precluded a firm assessment of ancestral states, although two widespread genera, Adenostemma and Mikania, were implicated as likely relatives of the aquatic lineages. Our data also support the continued recognition of Shinnersia and Trichocoronis, which occasionally have been considered synonymous, as distinct genera.