ISSR molecular markers with ninteen primers were used to analyze the genetic variation between 1 diploids and their 10 homological tetraploids of Isatis indigotica Fort..The results showed that genetic variation was distinct difference between diploids and their homological tetraploids of Isatis varied with different genotypes.In addition to the main genetic loci were same,some tetraploids amplified extra bands and some tetraploids with missing bands.There were polymorphic loci between the homological tetraploids.11 strains were detected 111 alleles,its homological tetraploid was 55.22%.The clustering results show that genetic variation is different between diploids and tetraploids.The genetic variation with medium is on the high side between diploids and tetraploids by ISSR.