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Phylogenetic analyses of the cpDNA trnQ-trnK 5′ exon region for 27 genera and 42 species of Saniculoideae and early diverging lineages of Apioideae were carried out to assess or confirm the tribal placements of the following anomalous genera: Annesorhiza, and Phlyctidocarpa. To accommodate these unique early diverging members of the Apiaceae and to reflect their relationships, a new tribal classification system has become necessary. Many of the early diverging genera (herein referred to as the protoapioids) can readily be distinguished from the euapioids (the remaining apioids) by the presence of scattered druse crystals in the mesocarp. The major morphological discontinuity within the family, however, lies between the combined protoapioids and euapioids (representing an expanded Apioideae s.l., including the Saniculoideae) and the subfamilies Azorelloideae and Mackinlayoideae. The broadened subfamily Apioideae is diagnostically different from the other subfamilies in the absence of rhomboidal crystals, the presence of druse crystals scattered throughout the mesocarp (subsequently lost in the euapioids), and the non-woody endocarp. No such diagnostic characters are available to support the traditional or recently expanded concept of Saniculoideae. The broadened concept of Apioideae is also supported by the sporadic presence of true wings. This character can be variously interpreted from a phylogenetic point of view, but nevertheless has considerable diagnostic value. A new tribal classification system for the protoapioids is proposed on the basis of molecular, morphological and anatomical evidence. This new system is intended to be practical and non-hierarchical to allow for future realignments amongst the tribes, as more evidence becomes available. It makes provision for hitherto poorly known African taxa and comprises the following eight tribes, five of which are newly described: Annesorhizeae, Choritaenieae, Heteromorpheae, Lichtensteinieae, Marlothielleae, Phlyctidocarpeae, Saniculeae and Steganotaenieae.