The Eriocaulaceae are easily recognized because of the small unisexual flowers in long–pedunculate heads and spiraperturate pollen grains. Their monophyly has never been disputed but internal relationships within the family have not been broadly explored and genera are typically distinguished by few floral characters. Here, we present the first comprehensive phylogenetic study of Eriocaulaceae based on individual and combined molecular datasets, including the plastid psbA–trnH and trnL–F and the nuclear ITS. Results are largely congruent among DNA regions and support the internal dichotomy between the two subfamilies: Eriocauloideae and Paepalanthoideae. Eriocaulon and Leiothrix are strongly supported as monophyletic, whereas Paepalanthus, Blastocaulon, and Syngonanthus are not monophyletic. The phylogenetic nature of Actinocephalus is not resolved and Lachnocaulon, Mesanthemum, Philodice, Rondonanthus, and Tonina (monospecific) are represented in our analyses by a single species each. Based on our results, we suggest two principal generic realignments in the family. The first is the division of Syngonanthus in two genera: Syngonanthus s.str., including Philodice (conserving the former name against the latter), and Comanthera, which is being reinstated to include two sections segregated from Syngonanthus: S. sect. Eulepis and S. sect. Thysanocephalus. The second realignment suggested is the amalgamation of Actinocephalus, Blastocaulon, Lachnocaulon, and Tonina into Paepalanthus s.l. Three 'stat. nov.' within Paepalanthus are published (P. ser. Leptocephali, P. ser. Rosulati, and P. ser. Dimeri).