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Premise of the Study: Microsatellite markers were isolated in Polemonium brandegei and P. viscosum to be used in future studies of mating system evolution, population structure, and hybridization., Methods and Results: Six loci were used in a preliminary genetic diversity study in two populations each of the closely related Polemonium brandegei and P. viscosum. We found 39 alleles across the six loci (average 7 per locus), with overall levels of observed heterozygosities ranging from 0.067 to 0.867 in P. brandegei and 0.000 to 0.666 in P. viscosum. Additional primers are reported, but require further design and optimization., Conclusions: The reported markers will aid in further studies of mating system evolution, population structure, and hybridization in P. brandegei and P. viscosum.