Sinoswertia tetraptera (Maximowicz) T. N. Ho, S. W. Liu & J. Q. Liu is an annual herb endemic to the Qinghai-Tibet Plateau. Here, microsatellite (simple sequence repeat, SSR) markers for S. tetraptera were developed in order to better utilize and protect this essential medicinal plant resource. Primers for 14 polymorphic and 2 monomorphic microsatellite loci were obtained based on restriction site-associated DNA se-quencing (RAD-seq). The 14 polymorphic loci were further investigated in 57 individuals from three natural populations of S. tetraptera. The number of alleles observed for these 14 loci ranged from 4 to 7 (mean: 5.071). The expected heterozygosity ranged from 0.003 to 0.312 (mean: 0.194), while the observed heterozy-gosity ranged from 0 to 0.281 (mean: 0.047). Three primers showed transferability to Halenia elliptica, a mem-ber of the subtribe Swertiinae (Gentianaceae). These polymorphic markers will be useful in future research on the population structure and genetic diversity of S. tetraptera.