Abstract: Twelve populations of Artemisia argyi and 22 SCoT primers were used as test material, the genetic diversity and population structure characteristics of the 12 populations were studied by methods of NTSYS-pc 2.1,Popegen 1.32,in order to provide reference for the breeding of new Ai varieties.The results showed that 87 alleles were detected by 22 SCoT markers, with an average of 3.95 alleles for each primers.The average PIC,I and H were 0.690,0.483 and 0.317 that showed high genetic diversity.The average value of Na, Ne, I and He per locus were 1.444,1.419,0.349 and 0.238,Anyang Tangyin population was the highest.Genetic similarity and the genetic distance were 0.795-0.975 and 0.025-0.229,with average of 0.909 and 0.097.Jiyuan and Huanggang Qichun populations had the highest and nearest genetic similarity coefficient and genetic distance.Gst of SCoT was 0.293,indicated a low level of genetic diversity among populations, and genetic differences for 9% was attributable to inter-population.Nm was 2.022 among 12 populations indicated that gene flow was lower among populations,resulting genetic difference was small among populations.Four classes were clustered at the genetic similarity coefficient of 0.914 including 8,2,1 and 1 population,respectively.