A phylogenetic study of plastid DNA sequences (ndhF, trnL/F, and rps16) in Lamiales is presented. In particular, the inclusiveness of Scrophulariaceae sensu APG II is elaborated. Scrophulariaceae in this sense are mainly a southern hemisphere group, which includes Hemimerideae (including Alonsoa, with a few South Americanspecies), Myoporeae, the Central American Leucophylleae (including Capraria), Androya, Aptosimeae, Buddlejeae, Teedieae (including Oftia, Dermatobotrys, and Freylinia), Manuleeae, and chiefly Northern temperate Scrophularieae (including Verbascum and Oreosolen). Camptoloma and Phygelius group with Buddlejeae and Teedieae, but without being well resolved to any of these two groups. Antherothamnus isstrongly supported as sister taxon to Scrophularieae. African Stilbaceae are shown to include Bowkerieae and Charadrophila. There is moderate support for a clade of putative Asian origin and including Phrymaceae,Paulownia, Rehmannia, Mazus, Lancea, and chiefly parasitic Orobanchaceae, to which Brandisia is shown to belong. A novel, strongly supported, clade of taxa earlier assigned to Scrophulariaceae was found. The clade includes Stemodiopsis, Torenia, Micranthemum and probably Picria and has unclear relationships to the restof Lamiales. This clade possibly represents the tribe Lindernieae, diagnosed by geniculate anterior filaments, usually with a basal swelling.

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Cladistic analyses by maximum parsimony and Bayesian inference methods of chloroplast and nuclear sequence data indicate a new position for Limosella (Scrophulariaceae). Following this result, a new circumscription of the tribe Limoselleae is presented where the tribe Manuleeae is included in Limoselleae. Further, the study discloses that the genus Sutera is paraphyletic in its present circumscription, but that the two sections of Sutera , Sutera and Chaenostoma , are monophyletic. To accommodate these findings the genus Chaenostoma is re-established. Furthermore, the genus Jamesbrittenia recently expanded by Hilliard is shown to be a highly supported monophyletic group in its current circumscription.

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