Lathraeocarpa acicularis, a small woody Rubiaceae endemic to Madagascar, was rediscovered after more than 50 years. A phylogenetic reconstruction based on four plastid markers (atpB-rbcL, rps16, trnL-trnF, petD) proves that its previous position within the monogeneric tribe Lathraeocarpeae can no longer be supported. Our data clearly show that Lathraeocarpa acicularis has its closest relatives among taxa of the Hedyotis-Oldenlandia group of the herbaceous tribe Spermacoceae sensu lato. The taxon falls within the Pentanopsis clade and is sister to a group comprising the Madagascan genus Gomphocalyx and the Afro-Madagascan genus Phylohydrax. A detailed survey of the morphology and anatomy of the genus based on our recently collected material of Lathraeocarpa acicularis is presented, providing additional arguments for the new taxonomic position.