Iron is regarded as one of the most important nutriments, and many diseases are related to iron deficiency or its overload. Approximately 70% of iron in the body is located in heme, functioning as hemoglobin, myoglobin, and cytochrome P450. Iron itself also has many catalytic functions through the iron-sulfa cluster. It is believed that iron and/or heme plays significant roles in regulation of genes, however, little about the mechanism has been elucidated. Recently, not only iron but also heme has been identified as important regulators of gene activation via oxygen sensing. For example, iron controls the oxygen response of HIF-1 activity by two mechanisms; in cytosol, the half life of HIF-1 alpha is determined by hydroxylation of Pro, and transcriptional activity of HIF1 alpha in nuclei is disturbed by hydroxylation of Asn. Hemoproteins in prokaryotes such as FixL, Dos, and HemAT were found to be oxygen sensors, however, little has been reported in eukaryotes. Our finding on Bach1 seems to be the first report of heme and oxygen-mediated regulation of genes in vertebrates. Understanding of these newly identified mechanisms in iron- and heme-controlled genes is essential in the field of nutritional science. We therefore summarize here the recent findings indicating mechanisms of iron as transcriptional regulators.