Primula sieblodii E. Morren is a perennial herb, classified as ‘Near Threatened’ in the Japanese Red List. Using the magnetic enrichment method, we have developed 120 microsatellite markers and screened polymorphisms within the species as a whole as well as within a single population. At the species level, the average number of alleles per locus, and the average observed and expected heterozygosities were 7.06, 0.48, and 0.74, respectively; at the level of the single population these values were 5.53, 0.52, and 0.64, respectively. The microsatellite markers presented here will be valuable research tools in forthcoming projects, such as QTL mapping as well as for association studies of P. sieboldii.