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.