Abstract: The circular dichroism (CD) and electronic absorption spectra of seven derivatives of shikonin and alkannin isolated from the roots of Onosma confertum W. W. Smith (from Sichuan) and Arnebia euchroma (Royle) Johust (from Xinjiang) were described. Each pair of CD spectra obtained was exact mirror images and the UV specra of these compounds were very similar. In comparison with the CD spectra of shikonin given in literature, the configuration of the pigments from Sichuan was assigned R and from Xinjiang were all S.