Miscanthus sinensis var. formosanus Hack is a grass species growing in 1200-2000 M elevation mountain areas in Taiwan, where the species grows is between the distribution of M. sincesis var. glaber (Naki) J. Lee and M. sincesis var. transmorrisonensis Hayata. In this study, isozyme electrophoresis was applied to detect the (1) genetic strusture of natural populations; (2) genetic variation of spike's offspring and (3) the genetic differentiation among these three varieties in species of Miscanthus sinensis in Taiwan. 16 loci from nine stains was used to analyze the isozymic variation of adult individuals, 6 loci from six stains for spike offspring. The results shown the average of expected heterozygosity (HE) is 0.202 and the coefficient of gene differentiation (GST) is 0.09, both demonstrated the similar parameter to mix-mating wind-pollinated species. The FST values from 6 populations of M. sinensis var. formosanus Hack are 0.093, which is higher than the genetic differentiation (FST=0.056) among the populations of the three varieties in Nantou. The higher FST is showing the gene flow among these three varieties is greater than other different populations of M. sinensis var. formosanus Hack. The estimation of multilocus outcrossing rate, tm=0.89, suggests an outcrossing mating strategy in M. sinensis var. formosanus Hack. In addition, the study of genetic variation from spike offspring indicated that genetic composition from a single spike is indistinguishable from its natural population, the genetic similarity is as high as 0.998. The genetic homogeneity implies a high gene flow within M. sinensis var. formosanus Hack population.