We conducted a genome-wide transcriptomic analysis in soybean leaves and roots treated with zinc (Zn) deficiency using RNA sequencing (RNA-seq) technology. Two biological replicates of RNA-seq were included for Zn-sufficient leaves (ZSL), Zn-deficient leaves (ZDL), Zn-sufficient roots (ZSR), and Zn-deficient roots (ZDR). Therefore a total of eight libraries were constructed. Using a 2-fold change and a P-value =0.05 as the cut-off for selecting the differentially expressed transcripts, we globally identified Zn-deficiency responsive genes. At least 20 genes that are potentially involved Zn homeostasis were significantly changed by Zn deficiency, including 7 ZIP (ZRT, IRT-related protein) transporter genes, 3 nicotianamine synthase genes, and 7 metallothionein genes. At least 48 genes encoding likely Zn-binding proteins were found to be responsive to Zn deficiency in leaves or roots. Eighty-five transcription factor genes were significantly changed by Zn deficiency in leaves or roots, including 5 bZIP members and 10 Golden 2-like members. In addition, some other groups of genes which are possibly related to reactive oxygen species scavenging, calcium and hormone signaling, and protein phosphorylation and dephosphorylation also differentially expressed under Zn deficiency. Overall design: The first trifoliate true leaves and roots of soybean were harvested after 12 days treatment with or without zinc element in the nutrient solution, and RNA was extracted and sequenced by paired-end sequencing. RNA sequencing reads were aligned against the soybean reference genome and differentially expressed genes between treatments were detected.