A molecular phylogenetic study based on nuclear ribosomal internal transcribed spacer sequences and plastid rps16 intron sequences on the status of the genus Gymnocarpos (Paronychioideae, Caryophyllaceae) is presented. Gymnocarpos decandrus and Sclerocephalus arabicus form a strongly supported clade within a well-supported group consisting also of G. przewalskii, and the rest of Gymnocarpos. Re-examination of morphological characters also supports this conclusion. Paronychia is found to be polyphyletic, with the subgenera Paronychia and Siphonychia forming a strongly supported sister group to Gymnocarpos, whereas P. kapela and P. chlorothyrsa (representing subgen. Anoplonychia) are found to be related to Herniaria and Philippiella. A key to the 10 species recognized in Gymnocarpos is presented, as well as synoptical information on nomenclature and distributions.