Polar auxin transport (PAT) is essential to control root growth. Flavonoids are widely thought to be PAT inhibitors leading to short root developments. However, we found that the flavonoids scutellarin and scutellarein, which both have a 6-hydroxyl group unlike the structure of known flavonoid-PAT-inhibitors, promote PAT in roots. They increase root length; rescue the short roots induced by the PAT-specific inhibitor TIBA; enhance the expression of the PAT mediators PIN1, PIN2 and AUX1; increase the auxin concentration at the quiescent center; and change the distribution of the meristem organizer WOX5. In contrast, rutin and naringenin, which have no 6-hydroxyl group and have different structural features in B-ring, shows the opposite/no effects. Our evidence suggests that flavonoids with and without a 6-hydroxyl group might result in opposite effects on root growth and thus act as chemical switches in regulating PAT.