Maximum likelihood and Bayesian analyses of nrDNA (ETS1f) and plastid DNA (rpl32-trnL, trnH-psbA) sequence data are presented for ‘C3Cyperus’ (Cyperaceae). The term ‘C3Cyperus’ indicates all species of Cyperus s.l. that use C3 photosynthesis linked with eucyperoid vegetative anatomy. Sampling comprises 77 specimens of 61 different taxa, representing nearly all previously recognized subdivisions of C3Cyperus and the segregate genera Courtoisina, Kyllingiella and Oxycaryum. According to our results, the Cyperus clade is divided in six well-supported clades. The first of these clades (clade 1) forms three subclades largely corresponding to Cyperus sections Haspani, Incurvi and Diffusi. Clade 2 comprises the entirely New World C. section Luzuloidei sensu Denton (1978). Clade 3 is a highly diverse clade including two subclades: clade 3a, C. sections Pseudanosporum and Anosporum plus the segregate genera Courtoisina and Oxycaryum; and clade 3b, C. section Fusci. Clade 4 corresponds to C. section Alternifolii and clade 5 to C. section Leucocephali plus the segregate genus Kyllingiella. The sixth clade is a well-supported monophyletic clade encompassing all C4Cyperus s.l. species (‘C4Cyperus’). This study establishes a phylogenetic framework for future studies. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 167, 19–46.