The cyclohexane (Ch) extracts of the roots of five Greek endemic Boraginaceae plants, Onosma kaheirei Teppner, O. graeca Boiss., O. erecta Sibth. & Sm., Alkanna sfikasiana Kit Tan, Vold and Strid and Cynoglossum columnae Ten, were investigated for the presence of alkannin/shikonin-related compounds. All species, s except C. columnae and O. erecta, were found to contain this type of compounds. Seven compounds were obtained after several chromatographic separations from the Ch extracts of the investigated plants: deoxyalkannin (1), 2″-( S)- α-methylbutyrylalkannin (2), isobutyrylalkannin (3), propionylalkannin (4), acetylalkannin (5), β-hydroxyisovalerylalkannin (6), and β,β-dimethylacrylalkannin (7). All structures were identified by 1D 1H-/13C- and 2D NMR spectroscopy, assisted also by ESI-MS. The extracts and the isolated compounds exhibiting an interesting antimicrobial profile when evaluated for their antimicrobial activity against six Gram-positive and -negative bacteria and three human pathogenic fungi.