• Premise of the study: Microsatellite primers were identified and characterized in Acca sellowiana in order to expand the limited number of pre‐existing polymorphic markers for use in population genetic studies for conservation, phylogeography, breeding, and domestication.• Methods and Results: A total of 10 polymorphic microsatellite primers were designed from clones obtained from a simple sequence repeat (SSR)–enriched genomic library. The primers amplified di‐ and trinucleotide repeats with four to 27 alleles per locus. In all tested populations, the observed heterozygosity ranged from 0.269 to 1.0.• Conclusions: These new polymorphic SSR markers will allow future genetic studies to be denser, either for genetic structure characterization of natural populations or for studies involving genetic breeding and domestication process in A. sellowiana.