Abstract: The genetic diversity and relationship of 14 Ginkgo biloba chichi clones were tested by AFLP. 8 primer combinations selected from 64 primer combinations produce a total of 935 bands, of which 920 bands were polymorphic, and accounted for 98.40%. It suggested that Ginkgo biloba chichi has a rich genetic diversity. The molecular genetic similarity coefficients ranged from 04404 to 07299, and that the average being 04752, indicating that genetic variation occurs among them. All of Ginkgo biloba chichi were clustered into 5 groups according to UPGMA cluster and principal coordinate analysis, but the clones from the same origin didn′t distribute in the same group totally. The result indicated that there′s no strict correlation between geographical and genetic diversity.