Background: the underlying mechanisms regulating biosynthesis and the very existence of a cellular system in plants have yet to be clarified to a satisfying point. Aim: this experiment tried to reveal the influence of cantharidin and endothall on gene expression of critical enzymes, glutathione S-transferase, protein phosphatase and, aspartate phosphatase in Cichorium intybus L., an important medicinal plant. Methods: two concentrations of cantharidin and endothall, 2.5 and 10 ?gml-1, were applied on C. intybus seedlings, and the changes in genes evaluated in shoots and roots. Results and Discussion: Cantharidin and endothall-treated seedlings had the lowest expression level of glutathione S-transferase in 2.5 ?gml-1 (0.92±0.11 and 1.07±0.61, respectively) while in 10 ?gml-1, the expression levels were slightly higher. The glutathione S-transferase expression in roots followed a similar trend. The Cantharidin effect on protein phosphatases in shoots and roots of C. intybus followed a similar pattern where the expression level of protein phosphatases in shoots and roots of treated seedlings with 2.5 ?gml-1 (0.51±0.03 and 1.34±0.12, respectively) reduced. At 10 ?gml-1 cantharidin, protein phosphatases' expression markedly increased in both shoots and roots (3.55±0.21 and 3.96±032, respectively). The expression of protein phosphatases in shoots received 2.5 ?gml-1 endothall considerably enhanced (43.21±3.1), whereas its expression was close to zero in roots. The expression of aspartate phosphatases in shoots with cantharidin 2.5 ?gml-1 was almost zero. Whereas in 10 ?gml-1, its expression was radically increased (3.76±0.23). Roots treated with cantharidin indicated high levels of expression, particularly in 10 ?gml-1 (2.07±0.11). Root treated with 2.5 ?gml-1 cantharidin similarly did not express aspartate phosphatases. Seedlings exposed to endothall, the relative expression level of aspartate phosphatases in shoots under 2.5 ?gml-1 was 17.49±1.21 while in roots with 2.5 ?gml-1 was down to 0.45±0.09. Conclusion: It can be reliably expressed that cantharidin and endothall halt plant growth in a dosage-dependent manner by downregulating critical enzymes C. intybus.