Carex sect. Ceratocystis is distributed in Eurasia and North America, with a few disjunct taxa in the Southern Hemisphere. Despite being one of the most intensively studied groups within Carex, its taxonomy remains a complex issue due to hybridization and faint morphological boundaries. Two main contrasting approaches to its taxonomy may be distinguished, synthetic and analytical, widely differing in the number of considered taxa. The status of several morphotypes from Europe and the Mediterranean Basin are particularly problematic. We used phylogenetic analyses of nuclear ITS and plastid rps16 and 5′trnK sequences along with cytogenetic data to evaluate the main taxonomic approaches and to infer evolutionary patterns in Europe and North Africa, with a special focus on the problematic morphotypes. Three major clades were found which mostly match morphological features of the utricle. Carex durieui should be excluded from section Ceratocystis. Although a linear agmatoploid series has been generally proposed to account for the cytogenetic evolution of section Ceratocystis, our results suggest chromosome number increase but not in a linear fashion. Different extensive hybridization areas in South Europe are suggested for some of the problematic morphotypes (Pyrenean-Cantabrian Mountains, Atlantic-Iberian Strip and Corsica).