Abstract: Aims Rhododendron liboense was a plant species with extremely small populations which distributed on top of limestone mountains, it has high ornamental and scientific research value. The habitat of it was fragile, and the wild population of it was rare, which urgently needs to be studied for conservation genetics. Methods This study focused on 43 individuals from three populations of R. liboense, using double digest restriction-site associated DNA sequencing technology (ddRAD-seq) to obtain single nucleotide polymorphism (SNP) data. The genetic diversity and structure of R. liboense population were analyzed, and historical population dynamics were inferred. Important findings The results showed that the genetic diversity of R. liboense was low (He = 0.139 62 ± 0.003 32, π = 0.157 64 ± 0.003 83), and the level of genetic differentiation between populations was moderate (FST = 0.075 8), The variation within the population (88.22%) is greater than the variation between populations (11.78%) . Structure analysis, PCA analysis, and cluster analysis were used to divide the three populations of R. liboense into two genetic groups. The analysis of population historical dynamics showed that the effective population size (Ne) of R. liboense had been continuously increasing since the last glacial period, which might be related to the gradual warming of the climate suitable for its survival. Based on the above research results and population status, it was recommended to divide the populations into two management units for on-site conservation, while strengthening research on artificial breeding techniques to assist in the ex-situ conservation and field return of R. liboense.

Key words: R. liboense, plant species with extremely small populations, genetic diversity, genetic structure, demographic history