AbstractPhylogenetic relationships of the two Malagasy Sapotaceae endemic generaCapurodendronandTsebonahave been unclear until now. Recent collections from Madagascar, as well as a better representation of the tribe Isonandreae, altogether 95 terminals, were used to estimate a phylogeny of subfamily Sapotoideae. We analysed sequences of nrDNA (ITS) and cpDNA (trnH‐psbA) with Bayesian inference and parsimony jackknifing. As in previous analyses, Sapoteae and Sideroxyleae are recovered monophyletic. In addition, Isonandreae, distributed in the Indo‐Pacific, is for the first time resolved as monophyletic and sister to Sapoteae. All Malagasy accessions ofCapurodendron, Tsebona, and a new species are grouped in another well‐supported clade. This clade is accommodated in a new tribe Tseboneae characterized by caducous stipules, 5‐merous flowers with quincuncial sepals, contorted aestivation of corolla lobes, absence of corolla appendages, one or three stamens opposite each corolla lobe, villous staminodes, seeds with an adaxial scar and plano‐convex cotyledons, lacking endosperm. The new species is described in the new genusBemangidia(B. lowryi) because it has a unique leaf venation for the tribe and combines different morphological features fromCapurodendronandTsebona. All three genera are well‐supported monophyletic groups.Bemangidia lowryiis threatened with extinction due to extensive ongoing forest destruction and is assigned a preliminary conservation status ofCritically Endangered.