Despite centuries of work, the basic taxonomic knowledge of the flora of the Iberian Peninsula is still incomplete, especially for highly diverse and/or difficult genera such as Carex. In this study, we conducted an integrative systematic study based on molecular, morphological and cytogenetic data to elucidate the taxonomic status of several problematic Carex populations from La Mancha region (S Spain) belonging to Carex sect. Phacocystis. These populations have been traditionally considered of uncertain taxonomic adscription, but close to C. reuteriana due to their morphological appearance and ecological preferences. A detailed morphological and cytogenetic study was performed on 16 La Mancha’s problematic populations (Sierra Madrona and Montes de Toledo) to compare them with the other Iberian sect. Phacocystis species. In addition, a phylogenetic analysis was conducted using two nuclear (ITS, ETS) and two plastid (rpl32‐trnLUAG, ycf6‐psbM) DNA regions, including representatives from all species of sect. Phacocystis. We found a significant degree of molecular and morphological differentiation that supports the recognition of La Mancha’s problematic populations as a new Iberian endemic species, described here as Carex quixotiana Ben.Benítez, Martín-Bravo, Luceño & Jim.Mejías. Our results reveal that C. quixotiana, unexpectedly, is more closely related to C. nigra than to C. reuteriana on the basis of phylogenetic relationships and chromosome number. These contrasting patterns reflect the taxonomic complexity in sect. Phacocystis and highlight the need for integrative systematic approaches to disentangle such complicated evolutionary scenarios.