A new genus, Lintersemina (Condamineeae, Rubiaceae), with a single species, L. chucuriensis is here described, based on recent collections made during a biological exploration to the Magdalena Medio Region of Santander Department, central portion of Colombia. This region is of high interest for both the high endemicity of its flora and fauna and the critical conservation status of this biodiversity due to high levels of deforestation. Lintersemina is unique within the tribe Condamineeae for the following combination of characters: axillary, long-pedunculate inflorescences, loculicidal capsules with 1-2 seeds per locule, and large navicular seeds. Based on phylogenies obtained using plastid and nuclear sequence data, the genus is positioned in the Condamineeae (subfamily Ixoroideae), as a sister group to the genera Simira and Parachimarrhis. This new genus is only known from two localities at the foothills of the Yariguíes National Park, in the municipalities of El Carmen de Chucurí and Zapatoca, at 400–800 m elevation, in forest undercanopy, near streams. Threats of deforestation and a very low population density were assessed, and this species classified as Critically Endangered (CR) following IUCN criteria. Full description and illustrations are also included.