The Caryophyllales are one of the major lineages of angiosperms, including some 12 000 species and well known families such as Amaranthaceae, Cactaceae, Caryophyllaceae, Droseraceae, Nyctaginaceae and Polygonaceae. Phylogenetic hypotheses based on molecular characters have led to their circumscription and have considerably improved our understanding of interfamilial relationships. For this study, we generated a data set of the non-coding and rapidly evolving chloroplast petB-petD region, consisting of a transcribed spacer and a group II intron for 87 taxa of Caryophyllales and 22 outgroups. In addition, we analysed a complementary matK data set with complete sequences of the coding region. Trees obtained from both markers were well resolved and especially petD data yielded a well supported backbone for the Caryophyllales. The order is constituted by two sister clades, caryophyllids and polygonids, the latter containing a carnivorous subclade. Both Molluginaceae and Phytolaccaceae had been considered as polyphyletic, but not as severely as is now evident from this study with improved taxon sampling. As a great surprise, the hitherto unsampled genus Microtea is found with high support in an isolated position as the fourth branch in the caryophyllid clade. On the other hand, Lophiocarpus as the second genus of the Phytolaccaceae subfamily Microteoideae is sister to an Aizoaceae-Nyctaginaceae-Phytolaccaceae lineage. In line with their morphological distinctness, Microteaceae are described as a new family. Our data further resolve a distinct Mollugo clade, whereas Hypertelis appears to have affinities with Limeum, suggesting an expanded Limeaceae.