Monocot plants produce numerous adventitious (crown) roots. The plant hormone auxin has positive effects on crown root formation, while cytokinin suppresses it. We have demonstrated that auxin-induced CROWN ROOTLESS5 (CRL5) regulates crown root initiation in rice through the induction of OsRR1, a negative regulator of cytokinin signaling. CRL5 overexpressing calli formed adventitious roots, although CRL5 overexpressing plants did not induce ectopic roots, suggesting that CRL5, which promotes de novo root initiation, might function only in de-differentiated cells. A radicle initiated normally in a crl5 mutant, in spite of the defect in crown root initiation, whereas crown roots, but not a radicle, were produced in a radicleless1 (ral1) mutant. A crl5 ral1 double mutant displayed an additive phenotype, showing that the formation of each root is regulated by different genetic mechanisms in rice.