The taxonomy of Linderniaceae has been considered difficult, particularly in the establishment of a stable generic framework. The prevailing approach in Australia and globally has been to adopt a broad concept of Lindernia encompassing several segregates that have at various times been recognised as genera or subgeneric taxa. A recent global conspectus drawing on molecular phylogeny returned Lindernia to a narrower circumscription and also retained several long-recognised and more recently established genera. It included a polyphyletic Vandellia, encompassing many Australian species previously accepted as belonging in Lindernia. Here, we test these generic concepts using the phylogenetic analysis of plastid matK DNA sequences, including representatives of Australian Linderniaceae. We propose a generic taxonomy that resolves existing polyphyly and balances the need for name changes against the information conveyed by generic names. Our concept of Lindernia recognises three monophyletic subgenera. Evidence is insufficient to determine whether Micranthemum should be subsumed in Lindernia or remains a close ally with a sister relationship to it. In light of our findings, we return most of the Australian species to Lindernia; we also establish for the first time: Lindernia subg. Ilysanthes (Raf.) Wannan, W.R.Barker & Y.S.Liang, based on Ilysanthes Raf.; a replacement name Yamazakia W.R.Barker, Y.S.Liang & Wannan for Tittmannia Rchb. nom. rej., with consequential combinations Y. viscosa (Hornem.) W.R.Barker, Y.S.Liang & Wannan, based on Gratiola viscosa Hornem. and Y. pusilla W.R.Barker, Y.S.Liang & Wannan, based on Gratiola pusilla Willd.; and, in expanding Torenia, the combination Tor. anagallis (Burm.f.) Wannan, W.R.Barker & Y.S.Liang, based on Ruellia anagallis Burm.f.