I investigated levels of genetic diversity, population genetic structure, and gene flow in Hostacapitata, a herbaceous perennial native to South Korea and southwestern Japan. Starch gel electrophoresis was conducted on leaves collected from 310 plants in 19 Korean populations. Twenty-two of 25 putative loci examined were polymorphic in at least one populatin and the mean number of alleles per locus was 1.65. In addition, mean expected heterozygosity within populations (Hep=0.153) was higher than average values for species with similar life history traits. Significant differences in allele frequency were detected between populations at all loci (P<0.01), and slightly over 30% of the genetic variation was found among populatins (GST=0.308). Indirect estimates of the number of migrants per generation (Nm) (0.506, calculated from GST; 0.852, calculated from the mean frequency of ten private alleles) indicate that gene flow is restricted among the isolated Korean populations of H. capitata. Factors contributing to the high levels of genetic differentiation among populations of H. capitata include small and discrete populations, human disturbance, and low frequencies of pollinator foraging behavior.