Shiraia bambusicola is a species of medicinal fungi which is parasitic on bamboos.The genus Shiraia is a monotypic genus in the phylum Ascomycota.Differences of colony appearances and ability to product hypocrellin among stains isolated from different collecting sites suggested a genetic differentiation among S.bambusicola stains.In order to understand the genetic differentiation of this fungal species, the genetic diversity of 107 individuals in 8 populations collected from Jiangsu, Anhui and Zhejiang provinces of Eastern China were studied by using inter-simple sequence repeat (ISSR) analysis.