Premise of the study:Microsatellite primers were designed for Calochortus gunnisonii (Liliaceae), a montane lily species of the central and southern Rocky Mountains, using next‐generation DNA sequencing. The markers will be used to investigate population structure, genetic diversity, and demographic history.Methods and Results:Thirteen polymorphic microsatellite loci were isolated from C. gunnisonii using Illumina MiSeq next‐generation DNA sequencing and bioinformatic screening. The mean number of alleles per locus ranged from 4.15 to 5.92 (avg. = 4.97). Observed and expected heterozygosity ranged from 0.077 to 0.871 and 0.213 to 0.782, respectively. The primers were also tested for cross‐species amplification value with C. flexuosus, C. nuttallii, C. kennedyi var. kennedyi, and C. subalpinus.Conclusions:These primers will be useful for genetic and evolutionary studies across C. gunnisonii's range within the southern and central Rocky Mountains. Furthermore, these markers have proven valuable for cross‐species amplifications within Calochortus.