We describe a new taxon of Gastrodia (Orchidaceae), G. × nippo-uraiensis from Yakushima Island. Gastrodia × nippo-uraiensis shows similar outer appearances with both G. nipponica and G. uraiensis. It could, however, be easily recognized by the 13-16 mm long perianth tube which is distinctly smaller than G. nipponica (Honda) Tuyama and distinctly larger than G. uraiensis T.C. Hsu & C.M. Kuo. In addition, G. nippo-uraiensis bears mixed or intermediate floral morphological characters between G. nipponica and G. uraiensis. Therefore, this taxon can be considered as a natural hybrid between G. nipponica and G. uraiensis. The morphological characteristics and illustrations of the new taxon, G. nipponica and G. uraiensis are provided.