Methyl jasmonate (MeJA) interacted significantly with both indole-3-acetic acid (IAA) and 6-benzylaminopurine (BA) to influence cell growth of cultured Onosma paniculatum cells. Cell growth decreased with increasing concentrations of MeJA from 0.004–4.45 μM with or without IAA and BA. The same concentrations of MeJA (0–4.45 μM) increased the cell growth with IAA and BA, when administered to the cultured cells in M₉ medium. This was found to enhance the production of shikonin. The optimum time for MeJA addition for enhanced shikonin formation was 4 d after cell inoculation in M₉ medium. Furthermore, shikonin formation was affected significantly by both MeJA/IAA and MeJA/BA combinations. Shikonin content was enhanced by increasing MeJA concentrations with IAA concentrations in the range of 0–28 μM and with BA concentrations in the range of 0–44.38 μM in MeJA/IAA and MeJA/BA experiments, respectively. The optimal combination of MeJA and IAA was 4.45 μM and 0.28 μM, while MeJA and BA concentrations of 4.45 μM and 2.22 μM were optimal for shikonin formation. The result also showed that MeJA increased phenylalanine ammonia-lyase (PAL) and p-hydroxybenzoic acid-geranyltransferase (PHB-geranyltransferase) activities during the course of shikonin formation, but decreased the activity of PHB-O-glucosyltransferase within 9 d after inoculation. These results suggest that enhanced shikonin formation in cultured Onosma paniculatum cells induced by MeJA involves regulation of the key enzyme activities.