The improvement of cereals for soil related abiotic stresses is one of the major challenges faced by crop scientists for the next decades. Hypoxic and excess iron tolerances are among the most important stresses affecting plants subjected to flooding. This work aimed to identify cis-regulatory elements (CREs) in promoters of up-regulated genes belonging to network signaling cascades in response to hypoxia and iron toxicity conditions. Microarray data from different experiments have been used to identify differentially expressed genes in rice (Oryza sativa L. ssp. japonica cv. Nipponbare). Up-regulated genes related to hypoxia response, ERFs, HSPs and network signaling cascades of response to oxidative stress and scavengers of reactive oxygen species were analyzed. A comparison of cross-talk signals and significant CREs allowed to identify the major factors involved in correlated responses and show that the majority of genes have between five and ten TF binding sites. An overview of the different approaches and the main challenges to understand the complex regulation mechanisms involved in the regulation of these stresses are presented.