Gene flow between sympatric congeneric plants is thought to be very common and may pose serious threats to endangered species. In the present study, we evaluate the genetic diversity and divergence of three sympatric Rhododendron species in Jiaozi Mountain using newly developed microsatellites through the Illumina MiSeq sequencing approach. Genetic diversity of all three Rhododendron species studied was moderate in comparison to genetic parameters previously reported from species of this genus. Inter-estingly, genetic structure analysis of the three species identified a possible hybrid origin of the threatened Rh. pubicostatum. This sympatry should be considered a unimodal hybrid zone, since Rh. pubicostatum is predominant here. Unimodal hybrid zones are uncommon in Rhododendron, despite the fact that hybridization frequently occurs in the genus. Issues pertaining to the conservation of Rh. pubicostatum resulting from admixture of genetic material from its parental species are discussed.