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The Didiereaceae of the Caryophyllales contains 20 species in three subfamilies: Calyptrothecoideae (2 species from the dry parts of tropical north-east Africa), Didiereoideae (11 species from semi-arid areas in Madagascar) and Portulacarioideae (7 species, mainly from the arid south-western Africa). We performed Bayesian inference and maximum likelihood analyses on data from six plastid DNA regions, trnL-trnF, trnT-trnL, trnS-trnG, trnQ(UUG)rps16, rps16 and rpl16, for 19 species of the Didiereaceae. Our analyses corroborated the monophyly of the Didiereaceae and of its three subfamilies with high statistical support and also elucidated the relationships within the Portulacarioideae. The family has a very disjunct distribution in Madagascar, East Africa and southern Africa. After the divergence of Portulacaria afra, the Portulacarioideae mainly diversified around the margins of the hyper-arid Namib Desert and its greatest diversity of four species is found on the southern edge of the Namib. We show that the two genera of the Portulacarioideae, Ceraria and Portulacaria, are not monophyletic and we transfer the five accepted species of Ceraria to Portulacaria.