The phylogeny of Cyperus and allied genera has been reconstructed using cladistic analysis of plastid rbcL gene, rps16 intron, trnL intron, and trnL-F intergenic spacer sequence data in 40 species of tribe Cypereae. Cyperus s.s. as currently circumscribed is not monophyletic because ten cyperoid genera are embedded within it. Eucyperoid Cyperus species (with a C3 anatomy, e.g. C. involucratus) and the genera Courtoisina, Kyllingiella and Oxycaryum form a clade that is sister to a clade comprising chlorocyperoid species (with a C4 anatomy, e.g. C. papyrus) and the genera Alinula, Ascolepis, Kyllinga, Lipocarpha, Pycreus, Remirea and Sphaerocyperus. The position of two species is uncertain; C. tenellus is resolved in a clade together with Isolepis although with typical cyperoid spikelets, whereas I. humillima is not resolved near either Isolepis or Cyperus s.l. © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society, 138, 145–153.