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Paris polyphylla var. yunnanensis is a traditional Chinese medicinal plant and is listed as vulnerable by the IUCN. This medicinal herb is well known for its analgesic and anti-inflammatory properties, most notably as an ingredient of the hemostatic compound "Yunnan Baiyao". However, over-exploitation of the plant for economic purposes is pushing the species to the brink of extinction. Therefore, there is an urgent need to develop conservation strategies for this endangered species, for example, through assessment of its genetic structure and diversity. Here, we developed ten novel polymorphic microsatellite loci. The characteristics of these markers were assessed in 60 individuals from South China. The number of alleles per locus ranged from 4 to 12, Observed and expected heterozygosity ranged from 0.303 to 0.969 and from 0.790 to 0.976, respectively. These markers will therefore be useful tools for future population genetic studies and for the conservation of genetic resources of P. polyphylla var. yunnanensis.