Abstract:Inter-simple sequence repeat (ISSR) markers were applied to investigate the genetic diversity and differentiation of five geographical populations of Artemisia sphaerocephala. Using 12 ISSR primers, 222 loci were observed in 108 individual, of which 218 were polymorphic. A high level of genetic diversity was revealed: PPB=98.20% and Shannon’s index I=0.315 4 at the species level. Based on Nei’s Gst value (0.076 7)and analysis of molecular variance (AMOVA ,Фst=7.96%), it showed that the most genetic variation existed within the populations. Furthermore, it revealed there were wide gene flows and little genetic differentiation among populations of A.sphaerocephala due to high genetic identity(>98%), small genetic distance and the high gene flows(Nm=3.008 2).