Goodyera ×tanakae is described as a new taxon based on molecular and morphological comparison with its closely related species G. foliosa, G. velutina, G. henryi and G. maximo-velutina. Detailed morphological examination has revealed that morphological characters of G. ×tanakae, such as leaf coloration and venation and the shape of lip and column, are intermediate between G. foliosa and G. velutina. Molecular data based on genome-wide markers using the next-generation sequencing platform (MIG-seq data) have also supported that G. ×tanakae is a natural hybrid between G. foliosa and G. velutina. Both maximum likelihood and Neighbor-Net phylogenetic analysis indicated that G. ×tanakae occupies an intermediate position between G. foliosa and G. velutina. The STRUCTURE analysis also showed that G. ×tanakae has genetic components of both G. foliosa and G. velutina. Therefore, we concluded that this taxon is a natural hybrid between G. foliosa and G. velutina based on morphological and molecular data. The taxonomic identity of its closely related species G. foliosa, G. velutina, G. henryi and G. maximo-velutina has also been discussed.