Summary Shikonin derivatives are natural naphthoquinone compounds and the main bioactive components produced by several boraginaceous plants, such as Lithospermum erythrorhizon and Arnebia euchroma . Phytochemical researches utilizing L. erythrorhizon and A. euchroma cultured cells both indicate the existence of a competing route branching out from the shikonin biosynthetic pathway toward benzo/hydroquinones. A previous study has shown that the branch point is a putative alcohol dehydrogenase converting ( Z )-3’’-hydroxygeranylhydroquinone [( Z )-3’’-OH-GHQ] to an aldehyde intermediate ( E )-3’’-oxo-GHQ. However, the enzyme involved in the branch reaction is not characterized at the molecular level yet. In this study, we clone a candidate gene belonging to the cinnamyl alcohol dehydrogenase (CAD) family, AeHGO , through coexpression analysis of transcriptome data sets of shikonin-proficient and shikonin-deficient cell lines of A. euchroma . In biochemical assays, purified AeHGO protein reversibly oxidizes ( Z )-3’’-OH-GHQ to produce ( E )-3’’-oxo-GHQ followed by reversibly reducing ( E )-3’’-oxo-GHQ to ( E )-3’’-OH-GHQ, resulting in an equilibrium mixture of the three compounds. Time course analysis and kinetic parameters show that the reaction with ( Z )-3’’-OH-GHQ is about twice as efficient as with ( E )-3’’-OH-GHQ, which leads to the predominance of ( E )-3’’-OH-GHQ and ( E )-3’’-oxo-GHQ in the equilibrium mixture. According to a previous report, ( E )-3’’-oxo-GHQ can be converted to deoxyshikonofuran, a hydroquinone metabolite produced by boraginaceous plants. Considering there is a competition for accumulation between shikonin derivatives and benzo/hydroquinones in both L. erythrorhizon and A. euchroma cultured cells, AeHGO is supposed to play an important role in the metabolic regulation of shikonin biosynthetic pathway.