A cladistic analysis based on rbcL gene sequences from a representative sample of 18 species yields three most parsimonious trees that strongly support monophyly of Selaginellaceae. Within Selaginellaceae, the morphologically distinctive subgenus Selaginella is resolved as sister group to a clade composed of all other species, here termed the rhizophoric clade. In the rhizophoric clade, subgenus Stachygynandrum is paraphyletic to subgenera Ericetorum, Tetragonostachys, and Heterostachys. Monophyly of Ericetorum and Tetragonostachys is strongly corroborated. Results support a close relationship between “resurrection plants” in Stachygynandrum and the mat‐forming or tufted drought‐tolerant species of Tetragonostachys, indicating a common origin of xerophytism in these groups. A close relationship for all isophyllous species, as hypothesized in many classifications, is not supported by the rbcL data. Leaf isophylly and reduction in Ericetorum and Tetragonostachys most probably represent independent reversals...