The purported hybrid origin of Goodyera × tamnaensis was tested based on morphological and molecular markers. Goodyera × tamnaensis shares several morphological characteristics with G. schlechtendaliana and G. velutina and is sympatric with them, raising the possibility of a hybrid origin. We investigated nuclear ITS sequences as well as three cpDNA intergenic spacer (trnH-psbA and trnS-trnG) and intron (trnL) sequences to document hybridization and the origin of G. × tamnaensis. In the ITS region of G. × tamnaensis, 28 nucleotide polymorphic sites were observed. Of these, G. × tamnaensis shares ten specific character states with G. schlechtendaliana, and two specific character states with G. velutina. These 28 nucleotide polymorphic sites were confirmed by the analysis of cloned sequences. Individuals of G. × tamnaensis have the plastid sequences of either G. schlechtendaliana or G. velutina. We found a correlation between the plastid sequence of an individual of G. × tamnaensis and its leaf morphology; leaves are most similar to the parental species that donated the plastid genome to the hybrid. Our molecular data support the view that G. × tamnaensis is a hybrid between G. schlechtendaliana and G. velutina, and that it has originated more than once.