Significance Roots produce hundreds to thousands of small molecules with unknown functions. We targeted the apocarotenoid pathway, which has been linked to numerous developmental processes in Arabidopsis , for a sensitized chemical genetic screen to identify regulators of root development. β-Cyclocitral, a small molecule derived from β-carotene, was identified as a regulator of root stem cell behavior in Arabidopsis as well as in rice and tomato. β-Cyclocitral promotes root stem cell divisions to enhance root growth and branching. In rice, β-cyclocitral enhanced both root and shoot growth during salt stress, which has important implications for agriculture.