Scutellaria orientalisandS. araxensisare perennial species of genusScutellaria(Lamiaceae) which produce some important pharmaceutical secondary metabolites. Four strains ofAgrobacterium rhizogenes(A4, A13, ATCC15834 and MSU440), three types of explant (stem, petiole and leaf), six concentrations of acetosyringone (25-150 mu M), two different co-cultivation methods (light and dark condition) and two co-cultivation media (full and half-strength MS) were used for optimization ofA. rhizogenesmediated transformation efficiency. Moreover, two inoculation approaches including immersion and injection as well as three infection period (5, 7 and 10 min) were examined. The molecular confirmation analysis of putative transgenic roots was performed by PCR using specific primers of therolB gene. The results revealed that the transformation efficiency was affected by bacterial strain, co-cultivation medium and type of explants. The highest transformation frequency of 93.3% was achieved on stem explants ofS. orientaliswith ATCC15834 strain, followed by MSU440, A13 and A4 with the frequency of 63.3%, 46.6% and 30%, respectively. InS. araxensis, the best transformation frequency of 76.6% and 43.3% were obtained on stem and petiole explants with MSU440 strain. 5 and 7 min for infection period significantly improved the transformation efficiency inS. orientalisandS. araxensisrespectively. Transformation rates of stem explants induced by ATCC15834, A4 and A13 strains were 53.3%, 36.6% and 20% respectively. Transformation frequency was significantly higher in half-strength MS, regardless ofA. rhizogenesstrains.