An electrophoretic analysis of isozymes was conducted on 11 populations of Agastache foeniculum maintained in the U.S. National Plant Germplasm System. Eleven enzyme staining systems, controlled by 19 putative loci, were assayed to estimate parameters of genetic diversity and to determine systematic relationships among populations of this prairie species. Polypmorphism was detected in seven putative loci: Cat1, Got1, Got2, Pgm2, Phi2, Tpi1, and Tpi2. Percentage of polymorphic loci and average number of alleles per locus for the species were 36.8 and 1.6, respectively. Total heterozygosity was 0.08. Partitioning of genetic variability was 0.63 and 0.37 among populations, respectively. Interpopulational values for Nei's genetic identity coefficients ranged from 0.878 to 1.000. Partitioning of total genetic variability (63% within populations) and values of inbreeding coefficients (F) close to zero suggest that A. foeniculum is a cross-pollinated species. Geographic distribution and possible human manipulation of the species may play important roles in the genetic differentiation of these populations.