Tree peonies are well known garden flowers and very important medicinal plants with some 1,000 cultivars. Most of the cultivars are believed to be of hybrid origin and their wild parents are suffering from severe depopulation. To rejuvenate the traditional cultivars and assess the genetic diversity of the critically endangered wild species for conservation purpose, it is crucial to use suitable molecular markers. In this study, we isolated 14 polymorphic microsatellite loci from an enriched genomic library. These loci were verified by re-cloning and re-sequencing and their characteristics were tested with 20 individuals. On average there are 5.5 alleles per locus, and mean values of observed heterozygosity and expected heterozygosity are 0.41 and 0.67, respectively.