The study set of simple sequence repeat (SSR) markers were developed using Restriction site Associated DNA (RAD) approach and Illumina pairedend sequencing to the whole genome of endangered plants Rhododendron molle G. Don. And it would provide technical support for further investigation of population structure and diversity of R. molle and other congener species from the evaluation of 63 individuals from three different populations. The results showed that: (1) the sequencing output generated a FASTQ file size of raw reads 7.653G bp, and the clean reads was to 7.513G bp. About 171.534 M bp of R. molle genome distributed over 498 252 contigs were obtained upon assembly of sequencing data. (2) After filtering and SSR detection, a final set of 11 687 simple sequence repeats with primers were obtained from 11 961 microsatellite loci. The dinucleotides motif unit were the most abundant (51.76%) repeat sequences. (3) 128 microsatellite markers were selected randomly to detect the polymorphism in 6 different individuals of R. molle, from which 20 polymorphic primers were identified. (4) Then the characteristics and availability of polymorphic primers were further evaluated in 63 individuals from three different populations. The number of alleles per locus ranged from 4 to 16, expected heterozygosity (H_e) values ranged from 0.489 to 0.908, respectively. Our result showed that the abundance of SSR existed in R. molle was moderate and the dinucleotides were the most abundan repeat sequences. It further confirms that the RADseq method is an efficient and costeffective means for SSR discovery, and these polymorphic microsatellite markers developed in this study will be useful for further investigation of population structure and diversity of R. molle and other congener species.