A new holomycoheterotrophic member of Burmanniaceae, Gymnosiphon syceorosensis, is described from Mt. Hamiguitan located on the island of Mindanao, Philippines. This species differs from the recently named G. philippinensis from Cebu in a number of quantitative and qualitative characters. Phenetic (neighbor-joining) and phylogenetic (maximum parsimony) analyses of characters from Asian and Australian Gymnosiphon species were conducted and diagnostic taxonomic features were discussed. This new species appears to be most closely related to G. affinis J.J. Sm. from New Guinea but differs in a number of floral features including inner perianth lobe shape, stamen position in floral tube, and anther connective shape.