Abstract: ISSR markers was used to measure genetic diversity and genetic structure of the 40 individuals from two natural populations of Pedicularis dunniana,one autogamous perennial herb.A total of 100 DNA fragments were scored from 8 ISSR primers,of which 62% were polymorphic.A low level of genetic(diversity) within populations was detected(PPB=27%,23%,respectively).An analysis of Molecular Variance(AMOVA) was used to apportion the variation within and among populations.Results indicated that most of the variation(74.62%) resided among the populations,while only a small amount of variation(25.38%) within the populations.Selfing is likely the factor resulting in the low level of genetic(diversity) within the populations.Genetic drift in small populations and probably founder effects might also be the most important reasons that may explain the current genetic structure of P.dunniana.