Allium naqabense Al-Eisawi & Omar is described and illustrated from Ras al-Naqab in southern Jordan. The new species is assigned to Allium L. sect. Molium G. Don of Allium subg. Amerallium Traub. Allium naqabense differs from the closely related species A. erdelii Zucc., A. papillare Boiss., A. qasyunense Mouterde, and A. negevense Kollmann by having glabrous leaves and by the pale yellow anthers and style that are included within the perianth. The most closely related species, A. erdelii, has leaves that are pilose on both surfaces and anthers that are exserted and yellow. Allium naqabense has glabrous leaves and included stamens. The new species is assessed as Endangered (EN), according to IUCN criteria.