Maximum likelihood and Bayesian inference analyses of nuclear ribosomal DNA (ETS1f) and plastid DNA (rpl32-trnL, trnH-psbA) sequence data are presented for 'C4 Cyperus' (Cyperaceae). The term 'C4 Cyperus' encompasses all species of Cyperus s.l. that use C4 photosynthesis linked with chlorocyperoid vegetative anatomy. Sampling comprises 107 specimens of 104 different taxa, including many of the subdivisions of C4 Cyperus s.s. and all C4 segregate genera (Alinula, Ascolepis, Kyllinga, Lipocarpha, Pycreus, Queenslandiella, Remirea, Sphaerocyperus and Volkiella). According to our results, C4 Cyperus is a well-supported monophyletic clade nested in C3 Cyperus. Despite the lack of resolution along the backbone of the C4 Cyperus clade and for some internal branches, several well-supported clades can be distinguished. The first clade in C4 Cyperus is formed by Cyperus cuspidatus and C.waterloti. Other recognizable and well-supported clades correspond to segregate genera, i.e. Ascolepis, Lipocarpha including Volkiella, and Kyllinga. Species of C4 Cyperus s.s. form a core grade in which the C4 segregate genera are embedded. Pycreus, the largest segregate genus composed of c. 120 species, is not monophyletic as it includes several C4 species of Cyperus s.s. This study establishes a phylogenetic framework for revising the classification and character evolution in Cyperus s.l. © 2013 The Linnean Society of London.