To authenticate Scutellaria scordifolia and its closely related species using ITS2 sequence.Total genomic DNA was isolated from Scutellaria scordifolia and its related species. Nuclear DNA ITS2 sequences were amplified and sequenced,and ITS2 sequences of the other species of plants were obtained in Gen Bank,The Kimura 2-parameter( K2P) distances were calculated. Identification analyses were performed using Neighbor-joining( NJ) and secondary structure of ITS2 sequence methods.The genetic distances of ITS2 between Scutellaria scordifolia and its closely related species were 0. 014 ~ 0. 141,which were obviously higher than those in the intra-species of Scutellaria scordifolia. The NJ tree and secondary structure of ITS2 sequence can distinguish Scutellaria scordifolia and its closely related species.ITS2 sequence can effectively and accurately identify the Mongolian medicinal plant Scutellaria scordifolia and its closely relatives.