Abstarct: Echinacea purpurea L. is a herbaceous and perennial herb belongs to the Asteraceae family. The roots contain important drug compounds such as alkaloids,chlorogenic acid and chicory acid. In many plants, in vitro hairy roots culture is an effective way to produce secondary mextabolites.The hairy roots formation in plants is the result of a plant disease that is caused by Agrobacterium rhizogenesis. When the bacterium infects the plant, the T-DNA, which is located between the TR and TL portions of the bacterium in the plasmid Ri, is transferred to the plant and placed in the nuclear genome of the host plant. In this study, leaves of leaf and hypocotyl extract from inoculum seedlings from 20 to 30 days of seedling Echinacea purpurea were inoculated with Agrobacterium rhizogenesis in vitro conditions of LAB 9402, A4, A13 and ATCC15834 strains. Hairy roots appeared 2 to 3 weeks after infection. The bacteria were removed by transferring the explants into the MS medium of 2.1 with antibiotic cefotaxime. In order to evaluate the exxpression of PAL, 4CL and C4H genes and measuring the amount of chicory acid in fennel plants, the SA and methyl jasmonate concentrations and the samples were taken 72 hours after treatment. results showed increase in gene exxpression of PAL, C4H and 4CL was higher for treated samples compared to control. The highest amount of chicory acid was obtained when the concentration of 250 μM of acetic acid and 200 μM of methyl jasmonate was used separately. So that the application of methyl jsmonate at a concentration of 200 μm in comparison with the concentrations of 100, 50 and the control sample increased the exxpression of all three genes . But the salicylic acid stimulant up to 250 μm resulted in increased exxpression of the three genes and the application of higher concentrations (500 μM) reduced the exxpression of genes The amount of Cichoric acid in a concentration of 250 μM of SA and 200 μM of methyl jasmonate was measured