The Lamiales are one of the largest orders of angiosperms, with about 22,000 species. The Scrophulariaceae, as one of their most important families, has recently been shown to be polyphyletic. As a consequence, this family was re-classified and several groups of former scrophulariaceous genera now belong to different families, such as the Calceolariaceae, Plantaginaceae, or Phrymaceae. In the present study, relationships of the genera Craterostigma, Lindernia and its allies, hitherto classified within the Scrophulariaceae, were analyzed. Sequences of the chloroplast trnK intron and the matK gene (approximately 2.5 kb) were generated for representatives of all major lineages of the Lamiales and the former Scrophulariaceae. Bayesian and parsimony analyses revealed two isolated lineages, one of which consists of Lindernia and its allies, the other of Gratiola and allies. Gratiola was previously assumed to be related to Lindernia and was therefore included here. It is proposed to treat the two clades as separate families, Linderniaceae and Gratiolaceae. For the Linderniaceae, several morphological synapomorphies exist in addition to molecular data, such as conspicuous club-shaped stamen appendages.