Abstract: OBJECTIVE To study the genetic variation between tetraploid and diploid Scutellaria baicalensis.METHODS ISSR molecular markers were used to study the genetic differences between tetraploid and diploid of Scutellaria baicalensis.RESULTS ISSR primers were screened from 100 primers for formal amplification, the percentage of polymorphism reached 84.2%. The variation range of genetic distance was 0.086 9-0.242 9. The UPGMA clustering tree divided the samples into two major groups. The diploid groups were clustered into one category, and the tetraploid were clustered into another.CONCLUSION There are genetic differences between tetraploid and diploid Scutellaria baicalensis Georgi, and ISSR molecular markers can effectively reveal the polymorphism among materials.