Carex sect. Confertiflorae s.l., contains ca. 40 species and diverse in E Asia. It has one of the most unstable delimitations in the literature, and the section was proposed to split into two sections up to five different ones. Recent phylogenetic reconstructions showed Confertiflorae s.l. not to be monophyletic. In this study we investigate the phylogenetic structure, morphological affinities, and biogeographic history of sect. Confertiflorae s.l. We performed a taxon-based approach to explore the morphological affinities of the species considered in sect. Confertiflorae. We studied macromorphological observations and micromorphology of the nutlets using SEM, and used five molecular markers to reconstruct the phylogeny. The placement of all the species on a previously published megaphylogeny was tested in a preliminary exploration using a scaffolding approach. Then a core of species was selected to run the main analyses. The phylogenetic analyses confirmed the polyphyly of sect. Confertiflorae s.l., whose representatives were found within five distinct clades, with sect. Confertiflorae s.s. and sect. Molliculae clades were found to be closely related and contained the majority of the species. The composition of the two clades agreed with the morphological structure of the group, and we confirmed an exclusive combination of features. The origin of the two clades was found to be in the early Pliocene while the majority of the diversification events within each clade took place during the Pleistocene. Eventually, we proposed the rearrangement of sect. Confertiflorae as previously conceived as three independent sections: sects. Alliiformes, Molliculae, and Paludosae.