Abstract: The restriction-site associated DNA sequencing(RAD-seq) technology was used to analyze simple sequence repeats(SSR) information of Halenia ellipitica D. Don; SSR markers for this species were developed based on RAD-seq data. We identified 6 201 SSR loci with at least 100 bp at two ends, including five types(di-nucleotide, tri-nucleotide, tetra-nucleotide, penta-nucleotide, and hexa-nucleotide). Primers of 3 865 loci were designed successfully. Among which, amount of tri-nucleotide SSR loci is the most. Repeat motif type number is 316, and type number of penta-nucleotide motif is the most(91). Afterward, 65 designed primers were randomly selected to represent the five SSR types, and tested using annealing temperature gradient PCR. Subsequently, 32 individuals from four natural populations of H. elliptica were employed to estimate the SSR primers that can be amplified. One monomorphic and 13 polymorphic SSR loci were developed according to the result of PCR and Polyacrylamide gel electrophoresis. The number of alleles of the 13 polymorphic SSR loci is high(mean 5.462), and no linkage relation was found(P<0.01); ten loci deviate from HWE(P<0.01) and have many homozygotes(observed heterozygosity mean of 0.226); the range of inbreeding coefficient is in -0.443-1(mean of 0.656); the gene flow N_m is 0.474.