Abstract:To study the genetic diversity of Scutellaria baicalensis G., 147 individuals from six populations were analyzed by inter-simple sequence repeat (ISSR). Eighteen primers were selected to produce highly reproducible ISSR bands. Among 485 amplified bands, 466 showed polymorphism, the percentage of polymorphic bands reached 96.08%. Nei’s gene diversity index and Shannon information index were 0.244 4 and 0.388 9, respectively. Number of alleles (Na) and effective number of alleles (Ne) were 1.993 8 and 1.383 9, respectively. Gst was 0.123 3, genetic identity (I) and genetic distance (D) were 0.951 5 and 0.050 1, respectively. The results showed that the collected germplasm resources of S.baicalensis had a high genetic diversity in general. There was a certain genetic differentiation and gene flow among different populations and the genetic variation was mainly within populations. Molecular clustering results showed that the same region germplasms were not clustered completely following the collection source. It may be related to folk culture introduction or less than normal for ISSR primers. The genetic diversity of S.baicalensis germplasm resources can provide a basis for the evaluation, preservation and breeding of new varieties in the future.