A wide range of environmental stresses lead to an elevated production of reactive oxygen species (ROS) in plant cells thus resulting in oxidative stress. The biological nitrogen fixation in the legume - Rhizobium symbiosis is at high risk of damage from oxidative stress. Common bean (Phaseolus vulgaris) active nodules exposed to the herbicide Paraquat (1,1 '-Dimethyl-4, 4'-bipyridinium dichloride hydrate) that generates ROS accumulation, showed a reduced nitrogenase activity and ureide content. We analyzed the global gene response of stressed nodules using the Bean CombiMatrix Custom Array 90K, that includes probes from some 30,000 expressed sequence tags (EST). The experimental design, based on circular hybridizations, included four conditions as, with two independent biological replicates and three technical replicates for each conditions. A total of 2418 differentially expressed genes (DEG) were identified among the different combinations. Our results showed good correspondence among both the GO term and the MapMan enrichment analyses highlighting DEG from PQ-treated nodules assigned to the functional super-categories: trans-membrane transport, hormone signal transduction, stress response, and regulation. In this work we analyzed the effect of VHb-expressing R. etli CE3 in the symbiosis of common bean plants under oxidative stress experimentally generated by the addition of PQ for 48 hours. We analyzed the transcript profile, via microarray hybridization, using the Bean CombiMatrix Custom Array 90K, that includes probes from some 30,000 expressed sequence tags (EST).