Geometric morphometrics (GM) is a powerful analytical tool that enables complete quantification of shapes. Its use in Botany has a great potential for complementing plant evolutionary and ecological studies. Taxonomic delimitation in Carex has been complicated due to reduction of characters and frequent homoplasy. This problem is more marked in cases where the species exhibit dwarfism. South America is the continent with the least understood Carex flora. The systematic relationships of some bizarre-looking groups were not unraveled until molecular phylogenetic studies resolved their relationships. In particular, there are two species only known from their type material whose affinities remain uncertain: Carexherteri and C.hypsipedos. These two taxa are acaulescent plants that respectively grow in the Uruguayan pampa and Peruvian high-altitude meadows. Recently, both species were ascribed to the Carexphalaroides group (subgen. Psyllophorae, sect. Junciformes) due to superficial morphological similarities, such as the androgynous peduncled spikes. However, their character combination is also coincident for its circumscription to sect. Abditispicae species. Nevertheless, in the absence of confirmation from molecular analyses, their placement must be considered preliminary until additional data can be provided. In this work we employ for the first time geometric morphometrics (GM) tools to assess the systematic affinities of two taxonomically problematic sedge species based on fruit shape. We compared utricle morphology of C.herteri and C.hypsipedos with that of C.phalaroides group and species in sect. Abditispicae. To this end we used GM and traditional morphometric approaches. Utricle shape variation along with other morphological features support the exclusion of these two species from the C.phalaroides gr. and, at the same time, show clear affinities of C.herteri to sect. Abditispicae. Carexhypsipedos remains as an incertae sedis species. Our work shows the potential utility of GM for the exploration of systematic affinities in sedges and in other graminoids.