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Premise Microsatellite markers were developed in the federally endangered species Liatris helleri (Asteraceae) to evaluate species boundaries with closely related congeners within the genus. Methods and Results Using Illumina data, 17 primer pairs were developed in populations of L. helleri. The primers amplified motifs from tri‐ to hexanucleotide repeats with one to 17 alleles per locus. Primers were also tested for cross‐amplification in L. aspera, L. microcephala, and L. pycnostachya. Conclusions The developed primers for L. helleri serve as a novel genetic tool for future investigations in this genus, allowing for more explicit species delineation as well as population genetic analyses.