Despite centuries of intense 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. A detailed morphological and cytogenetic study was performed with 16 sampled La Mancha problematic populations (Sierra Madrona, Montes de Toledo) in order 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‐trnL^UAG, ycf6‐psbM) DNA regions, including representatives from the whole sect. Phacocystis. We found a significant degree of molecular and morphological differentiation that supports the recognition of these populations as a new Iberian endemic species, Carex quixotiana. Our results reveal that, unexpectedly, C. quixotiana is more closely related to C. nigra than to C. reuteriana on the basis of phylogenetic relationships and chromosome number. However, the overall morphological appearance and ecological preferences were misleadingly suggesting affinities with C. reuteriana. These contrasting patterns reflect the taxonomic complexity in sect. Phacocystis and remark the need of integrative systematic approaches to disentangle fiendish evolutionary scenarios.