Background and aims – The Paleotropical tribe Vanguerieae (Rubiaceae) is centred in Africa and Madagascar. In Madagascar, many of its ca 150 species are functionally dioecious, belonging to the small genus Bullockia and two large genera, Pyrostria (~90 species) and Peponidium (~50 species). These species estimates include many undescribed species, two of which are formally described here. Material and methods – A Bayesian inference of ITS sequence data from Vanguerieae was performed to pinpoint the generic placement of the new taxa. Morphological studies were conducted based on standard methods of herbarium taxonomy. The new species are described in detail, illustrated, and compared to morphological similar species. Distribution maps are presented and the preliminary conservation status of the new taxa was evaluated using IUCN criteria. Key results – Two new species of Malagasy Vanguerieae are described. ITS data place one in the genus Peponidium and one in the genus Pyrostria. Peponidium calciphilum sp. nov. is endemic to the Tsingy of Ankarana in northern Madagascar, while Pyrostria multilocellata sp. nov. is restricted to the spiny thickets in dry southern and southwestern Madagascar. Both species occur on limestone and in dry vegetation types, have 4-merous, functionally dioecious flowers, and bilocular fruits. Peponidium calciphilum sp. nov. is characterized by ovate, sessile leaves with cordate bases, well-developed subulate stipules, glabrous shoots, ovaries, and calyces, distinct tufts of hairs at the tips of the calyx lobes, and vaulted corolla lobes with well-developed appendages. Pyrostria multilocellata sp. nov. is characterized by very small, strongly coriaceous to almost succulent leaves, single-flowered male and female inflorescences, minute flowers, and multilocellate anthers in the male flowers. Peponidium calciphilum sp. nov. is considered as Endangered, whereas Pyrostria multilocellata sp. nov. is estimated to be Near Threatened.