PremiseMicrosatellite primers were developed for Puya raimondii (Bromeliaceae), an endangered species distributed in the Andean Mountains of Bolivia and Peru.Methods and ResultsGenome skimming of P. raimondii, P. macrura, and P. hutchisonii resulted in the selection of 46 pairs of cross‐species microsatellite markers. Of these, 12 microsatellite primer pairs produced clear and polymorphic bands in P. raimondii. These primer sets were then used for the detection of potential polymorphisms in 84 P. raimondii individuals collected from four populations in Peru. The number of alleles per locus ranged from one to six, and the observed and expected levels of heterozygosity ranged from 0.000 to 0.8929 and from 0.000 to 0.7662, respectively.ConclusionsThe microsatellite markers developed in this study will be useful for future population genetic analyses and breeding system studies in P. raimondii.