Promoting initiation and biomass production of roots is significant for plant-based industries including using roots as bioreactors. We used two citrus genotypes, Carrizo and US-897, as model plants to test the effects of root-predominantly overexpressed the iaaM (indoleacetic acid-tryptophan monooxygenase) gene and a CKX (a cytokinin oxidase/dehydrogenase) gene. The iaaM transgenic lines exhibited markedly faster root initiation, more root numbers, and higher root biomass compared to their wild-type counterparts. The transgenic iaaM + CKXplants also exhibited similar phenotypes, albeit to a lesser extent than the iaaMplants. Molecular analysis revealed an auxin-responsive CsGH3.1 gene was up-regulated in the iaaM roots and iaaM + CKX roots, and a cytokinin-responsive gene CsARR5 gene was down-regulated in the iaaM + CKX roots. Our results demonstrate that root predominant overexpression of the iaaM or both the iaaM and CKX genes drastically enhances the initiation, growth and biomass production of roots. These results provide additional support that manipulation of auxin and cytokinin levels in roots via transgenic or gene-editing technologies may benefit production of high-value secondary metabolites using roots as bioreactors and also improve rooting of recalcitrant plant species.