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PremiseThe genusAntennariahas a complex evolutionary history due to dioecism, excessive polyploidy, and the evolution of polyploid agamic complexes. We developed microsatellite markers fromA. corymbosato investigate genetic diversity and population genetic structure inAntennariaspecies. Methods and ResultsTwenty‐four novel microsatellite markers (16 nuclear and eight chloroplast) were developed fromA. corymbosausing an enriched genomic library. Ten polymorphic nuclear markers were used to characterize genetic variation in five populations ofA. corymbosa. One to four alleles were found per locus, and the expected heterozygosity and fixation index ranged from 0.00 to 0.675 and −0.033 to 0.610, respectively. We were also able to successfully amplify these markers in five additionalAntennariaspecies. ConclusionsThese markers are promising tools to study the population genetics of sexualAntennariaspecies and to investigate interspecific gene flow, clonal diversity, and parentage ofAntennariapolyploid agamic complexes.