• Premise of the study: Microsatellite primers were developed in the tree peony, Paeonia suffruticosa, to perform paternity tests as well as assignment to variety in special Austrian collections.• Methods and Results: Using SSR‐enriched libraries and EST‐mining, 8 polymorphic primer sets were identified in Austrian collections of Paeonia sect. Moutan DC. The primers amplified di‐ and trinucleotide repeats with 2–6 alleles per locus. All primers also amplified in P. ostii, P. pontaninii var. trolloides, P. delavayi, and P. lutea, and in the herbaceous species P. peregrina and P. tenuifolia (Paeonia sect. Paeon).• Conclusions: These results show the usefulness of primers in P. suffruticosa for population genetic studies and their ability to cross amplify in related taxa across the genus.