Our results demonstrate that the flavonoids biosynthetic pathway can be effectively manipulated to confer enhanced plant root growth under water-stress conditions. Abscisic acid (ABA) is one of most important phytohormones. It functions in various processes during the plant lifecycle. Previous studies indicate that ABA has a negative effect on root growth and branching. Auxin is another key plant growth regulator that plays an essential role in plant growth and development. In contrast to ABA, auxin is a positive regulator of root growth and development at low concentrations. This study was performed to help understand whether flavonoids can suppress the effect of ABA on lateral root growth. The recessive TRANSPARENT TESTA GLABRA 1 (ttg1) mutant was characterized on ABA and sucrose treatments. It was determined that auxin mobilization could be altered by modifying flavonoids biosynthesis, which resulted in alterations of root architecture in response to ABA treatment. Moreover, transgenic TTG1-overexpression (TTG1-OX) seedlings exhibited enhanced root length and lateral root number compared to wild-type seedlings grown under normal or stress conditions. Genetic manipulation of the flavonoids biosynthetic pathway could therefore be employed successfully for the improvement of plant root systems by overcoming the inhibition of ABA and some abiotic stresses.