Numerous microsatellite markers were developed forAquilegia formosafrom sequences deposited within the Expressed Sequence Tag (EST), Genomic Survey Sequence (GSS), and Nucleotide databases in NCBI. Microsatellites (SSRs) were identified and primers were designed for 9 SSR containing sequences in the Nucleotide database, 3803 sequences in the EST database, and 2226 sequences in the GSS database. For validation purposes, 45 primer pairs were used to amplify DNA from 16A. formosaindividuals from the H. J. Andrews experimental forest in Oregon, a Long Term Ecological Research (LTER) site. Genetic polymorphisms were identified at 30 of the 45 microsatellite loci with an average of 13.2 alleles per locus, and the observed level of heterozygosity was greater than 0.8 for 21 of the 30 loci. The use of these polymorphic loci was sufficient to individually separate the 16 individuals using a principal coordinate analysis. This comprehensive collection of primers significantly increased the availability of microsatellite primers forAquilegiaspp. and provided ample material for future studies that required highly variable SSRs such as mapping and association studies and investigation of plant mating system and gene flow.