Rhododendron×duclouxii is morphologically intermediate between Rhododendron spiciferum and Rhododendron spinuliferum, and was suspected to be a natural hybrid between these species. In this study, the nuclear ribosomal internal transcribed spacer (ITS) and chloroplast trnL-F regions of 34 accessions of R. ×duclouxii and its putative parents were analyzed for evidence of hybridization. The results from molecular data supported by morphology demonstrated that R. ×duclouxii represents a natural hybrid between R. spiciferum and R. spinuliferum. It also implies that the hybridization between R. spiciferum and R. spinuliferum is bidirectional, and that populations of R. ×duclouxii represent hybrid swarms from backcrossing or selfing of F1 plants. The study is important for understanding the speciation processes in the genus since it demonstrates for the first time the existence of a natural homoploid hybrid in Rhododendron subgenus Rhododendron.