This is the first study of the genetic diversity and structure of the big tree rhododendron, Rhododendron protistum var. giganteum, which is a highly endangered species with only two known endemic populations in a small area in the southern part of Yunnan Province in China. We detected moderate to high genetic diversity at the species level, but low genetic differentiation between the two extant populations. These results suggest that some rare and endangered species are able to maintain high levels of genetic diversity even at small population sizes.