A new species of Gymnosiphon Blume (Burmanniaceae), G. mayottensis Cheek, sp. nov. is formally described from Mount Bénara and Mount Mtsapéré on the island of Mayotte in the Comores. This is the first named species of the genus published from the Comoro Islands. The new species resembles G. longistylus (Benth.) Hutch. in the six long, filamentous, stigma appendages, two arising from each of the three styles, also in the absence of an underground tuber or thickened rhizome; it differs in that the bracts are appressed to the rhachises, and about equal in length to them (not patent, and < ¼ as long), the outer tepals turn rapidly from white to translucent at anthesis (not remaining white), the inner perianth lobes are absent (not present and conspicuous), the stigmas are broader than long, held horizontally and are united along their lateral margins (not longer than broad, pendulous, free from each other along their lateral margins). The new species is known from two forest sites, both with threats, and less than 50 individuals are known. Accordingly, it is assessed as Critically Endangered (B1ab(i-iv), B2ab(i-iv), D) using the IUCN 2012 standard. The new species is illustrated by colour photos and line drawings, and mapped.