Carex section Junciformes is one of the most diverse groups of the genus in South America, consisting of approximately 30 species. Here we describe a new species, Carex recondita, belonging to this section. We studied its placement within a molecular phylogeny of the group and found it to constitute an independent lineage. The new species is morphologically very close to C. austroamericana, from southern Patagonia, despite being phylogenetically divergent to the rest of Patagonian species of sect. Junciformes. So far, this species is known only from a few specimens recently collected in its type locality, despite growing in a well-collected area in the Andes of Metropolitana Region of Santiago, the most populated administrative region of Chile. We provide a detailed morphological description, comments on its relationship with other Southern Cone species of sect. Junciformes and relevant ecological notes.