Abstract: Rhododendron sinofalconerihas high ornamental value with its pure yellow flower and bell-shaped corollas clustered on the top of the branches. In recent years,due to the anthropogenic impact of road construction,illegal excavation and other human activities,its habitat was severely fragmented and its population was shrunk. Therefore,it was urgent to research on conservation biology of R.sinofalconeri. Singlenucleotide-polymorphism（SNP）site mining and genetic diversity analysis were performed on two surviving populations of Laojunshan（LJS）and Daheishan（DHS）using genotyping-by-sequencing（GBS）technology. As a consequence,analysis of the 103 133 high-quality SNPs revealed that the two populations had lower genetic diversity at the species level（Ne=1.308 6,Ho=0.187 8,and He=0.185 6）,and higher genetic differentiation（Fst=0.176 5）at population level. The value of gene flow（Nm）between populations was 1.167 4. By cluster analysis,principal component analysis and population genetic structure analysis,36 individuals were clustered into two different genetic groups. This study revealed the current situation of relatively low genetic diversity of R.sinofalconeri for the first time,which was helpful to further understand the endangered and scientific formulation of conservation measures.