Nitrogen fixation can improve the sustainability of agricultural systems by reducing the dependency on manure or synthetic nitrogen fertilizers. Aerial roots, a unique feature of certain maize and sorghum accessions, have been identified recently as unique sites for hosting nitrogen-fixing bacteria (diazotrophs) [1,2]. After the rain, thick aerial roots of these crops produce an abundant mucilage that provides a perfect environment for diazotrophs to fix nitrogen and transfer it to the plant. We used genomic and transcriptomic approaches to identify key genes associated with aerial root development and mucilage production in maize and sorghum. Using association and linkage mapping, we identified genetic loci that control the number of nodes developing aerial roots and the aerial root diameter. Using single-cell RNAseq, we identified cell-type specific gene regulatory networks involved in water perception and mucilage production. Finally, we proved that high rates of nitrogenase activity occur in the mucilage through acetylene reduction assays. Furthermore, we confirmed the transfer of this fixed nitrogen to the plant by enriching with 15N gas. Our findings also revealed that certain sorghum accessions acquire as much as 43% of their nitrogen from the atmosphere, as demonstrated by 15N isotope dilution experiments. Altogether, our studies are expected to reveal the genetic networks required for the establishment of this symbiotic relationship in these crops that have the potential to enhance nitrogen fixation in cereals and improve agricultural sustainability.