Abstract: The sporophores of Amanita parvipantherina are highly diversified by different collecting areas.The genetic diversity and clustering analysis of A.parvipantherina populations collected from 12 different areas were carried by using ISSR and ITS molecular markers in this study.The results were as follows:A.parvipantherina had high gene diversity,of which,57.4% existed within populations,and 42.6% among populations with geographical isolation,as the percentage of polymorphic band(PPB) amplified by 12 ISSR primers was 72.84%,and Gst among population was 0.426 1;The length of ITS sequences from the 12 samples was all 710 bp,and 30 base locus of ITS1 region had mutation;The results of both genetic distance analysis and clustering analysis were similar,which indicated the correlation between the genetic differentiation of A.parvipantherina and their geographical distribution;To the ability of revealing the genetic variation and genetic differentiation in this study,ISSR showed stronger resolution than ITS.