Rheum tanguticum (Polygonaceae), a plant species used in both traditional Chinese and Tibetan medicine, has been listed as endangered species because its distribution in the Tibetan Plateau has rapidly decreased in recent years. We estimated the genetic diversity of R. tanguticum using the cpDNA trnL-F region for 95 individuals from nine populations. The results demonstrated high genetic diversity in this species (Ht = 0.632), primarily due to variation among populations (68.4%, GST = 0.6839), as opposed to variation within populations (31.6%, Hs = 0.2). AMOVA analyses indicated that genetic differentiation among populations was very high (FST = 0.7009), and gene flow among populations was low (Nm = 0.11). The reason for high genetic differentiation among populations might be due to the geography of the alpine environment of the region and human activity. Furthermore, genetic structure in R. tanguticum implies that wild populations with high genetic diversity should be protected, and collecting seeds from populations with high genetic diversity is necessary for conservation breeding programs.
• High genetic diversity and large genetic differentiation among populations were observed in Rheum tanguticum. • The main reason for the observed genetic structure might be the geography of the alpine environment and human activity. • Conservation plans for in situ and ex situ protection were proposed.