Background and aims - Recent molecular studies validate a broad definition of Cyperus (Cyperaceae) uniting genera previously scattered in Cyperoideae. First indication of their affinity with Cyperus was obtained through embryography. Cyperus consists of a paraphyletic C3 Cyperus and monophyletic C4 Cyperus. In this study, we aim to check and clarify the putative positions of the segregate genera in C3 Cyperus. Additional information is given and remarks are made on the position of some as yet unplaced species or sections in the C3 Cyperus phylogeny. Methods - Embryos of Cyperus constanzae and C. gardneri were cleared and drawn. Inflorescences of selected C3 Cyperus species were investigated using scanning electron and light microscopy. Histochemical tests were performed to assess the presence of suberin in the 'corky' tissue of the nutlets of Cyperus pectinatus. Key results - Embryography not only supports tribal classification in Cyperoideae, it is also phylogenetically informative in C3 Cyperus. Morphology and ontogeny support molecular phylogenetic results suggesting the inclusion of the segregate genera in C3 Cyperus as new sections or in established sections, and confirm the need to broaden the circumscription of some of these sections. Conclusion - Although less diverse than C4 Cyperus, C3 Cyperus includes clades which evolved an exceptional morphological diversity compared to its limited species numbers. The segregate genera Courtoisina (deciduous spikelets), Kyllingiella (spirally-arranged glumes) and Oxycaryum (spirallyarranged glumes and dorsiventrally flattened dimerous gynoecia), and the taxon Anosporum (recognised at sectional, subgeneric or generic level) are here included in C3 Cyperus (= Cyperus subg. Anosporum) as sections or included in an existing section (Kyllingiella is included in Cyperus sect. Leucocephali). A formal taxonomic revision is presented with relevant new names and combinations, synonyms, diagnoses and identification keys