Coordinated functioning of the cob and florets of the maize ear confers grain yield. However, comprehensive molecular differentiation of the cob and florets and their responses to low nitrogen (LN) stress remain elusive. We compared transcriptional profiles of the cob and peripheral florets of a maize hybrid at the silking stage at two N levels in the field and found 1,864 differentially expressed genes between the cob and florets, with 1314 genes up-regulated in the cob and 550 genes up-regulated in florets. The cob was featured by preferential expression of 161 genes, with striking enrichment of genes that are involved in transport facilitation and energy metabolism, consistent with the physiological role of the cob in C/N storage and transfer during ear development. The florets were characteristic of preferential expression of 108 genes, with enrichment of genes that are involved in the cellular process and lipid biosynthetic process. LN caused differential expression of 588 genes in the cob and only 195 genes in florets, indicating that the cob dominated the response of the ear to LN at the transcriptional level. Differentially expressed genes under LN were involved in C/N metabolism, transcriptional regulation, development, cell rescue and defense, and signal transduction in the cob and/or florets. The expression level of 106 genes was regulated by LN in both tissues, suggesting a common regulatory network in these two functionally distinct tissues under LN. Compared with P or K deficiency, LN specifically caused differential expression of 14 genes, revealing unique biological consequences in the ear caused by N limitation at a critical reproductive stage. Collectively, our studies identified unique transcriptomic signatures of the cob and florets, revealed the dominance of the cob in response to LN at the silking stage, and provided molecular markers for N nutritional diagnosis and N efficient maize breeding. Overall design: Using Digital Gene Expression technology to compare the genome-wide gene expression profiles in cob and peripheral florets of a maize hybrid at the silking stage at two N levels in the field.Three biological replicates were generated for each sample.