Abstract: ISSR(inter-simple sequence repeat) markers were used to analyze the genetic diversity and patterns of population structure within and among nine populations of Gastrodia elata Bl.,a Chinese traditional herb in Guizhou Province,southwestern China.120 discernible DNA bands ranging in size from 200 to 1 600 bp were generated by 12 ISSR primers,97 of the bands(80.83%) were polymorphic,indicating considerable genetic variations at the species level.In contrast,ISSR diversity within populations was lower than that among populations,there were relatively low levels of polymorphism at population level with the percentage polymorphi loci(PPL) ranging from 17.5% to 40.83%,averaging 25.56%.Based on Nei's G_st value calculated by POPGENE1.31,genetic diversity(H_e) ranged from 0.042 to 0.153,averaging 0.073,Shannon information index was 0.332 6±0.224 1 at species level.The genetic differentiation(G_st) was 0.637 7, indicating that there was 63.77% of the variance among populations and 36.23% of the variance within populations.Restricted gene flow(N_m=0.284 1) among populations was a plausible reason for the high genetic differentiation observed for the species.The limited gene flow may result from several factors,such as seed dispersal,poor seed viability and isolation of population.