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Premise of the study: Microsatellite loci were isolated and characterized for population genetic studies of <i>Alpinia oxyphylla</i> (Zingiberaceae), a perennial rhizomatous herbaceous plant often used medicinally in China. Methods and Results: A total of 85 loci were identified using a magnetic bead enrichment method, of which 23 were polymorphic. The level of polymorphism was characterized in 32 individuals from two populations; the number of alleles per locus ranged from 1 to 13; and observed heterozygosity and expected heterozygosity varied from 0 to 1 (mean: 0.6441) and 0 to 0.887 (mean: 0.6241), respectively. Conclusions: The polymorphic microsatellite markers generated from this study will be useful for genetic diversity and structure analysis of <i>A. oxyphylla</i>.