AFLP analysis of genetic variation in wild populations of five Rhododendron species in Qinling Mountain in China

► Genetic variation of wild Rhododendron populations in Qingling Mountain was evaluated by AFLP. ► High levels of genetic diversity of the five Rhododendron species were detected. ► Genetic variation within the population was higher than that among populations. ► Data reported here are useful for evaluation and conservation of Rhododendron germplasm in China.