A new species of Gymnosiphon Blume (Burmanniaceae), G.fonensis Cheek is formally described from the Foret Classee de Pic de Fon, Simandou Range, Guinea-Forestiere, Republic of Guinea (Guinea-Conakry) in West Africa. The new species was formerly confused with and resembles G. bekensis Letouzey of central Africa in the broad flat outer tepal lobes, perianth tube >10 mm long, and (sub)sessile flower. It differs e.g. in that the length of the corolla tube, (13-)14-18 mm, exceeds the corolla diameter (10-11 mm) (vs length of the corolla tube (12 mm) < the corolla diameter (12-15 mm)), the anthers inserted c. 4 mm deep in the corolla tube (vs inserted at the corolla mouth) and the rhizome lacks scale-leaves (vs scale leaves present). Gymnosiphon fonensis is the first known species of its genus and family in which secondary pollen presentation has been recorded. The species is known from five sites, all with threats, in a single threat-based location, accordingly it is assessed as Critically Endangered (CR B1ab(iii)) using the IUCN 2012 standard, making it the most threatened species of Gymnosiphon in continental Africa. The new species is illustrated by colour photos and line-drawings and is mapped. An identification key is provided to the ten species of the genus now known from Africa-Madagascar.