Rhizobia are legume bacterial symbionts that fix nitrogen in the root nodules of plants. The aim of the present study was to investigate the global transcriptional response of rhizobia upon an acidic shock. Changes in the transcriptome of cells of Mesorhizobium loti strain MAFF303099 upon an acidic shock at pH 3 for 30 min were analysed. From a total of 7,231 protein-coding genes, 433 were found to be differentially expressed upon acidic shock, of which 322 were overexpressed. Although most of the overexpressed genes encode hypothetical proteins, the two most represented Cluster of Orthologous Group (COG) categories are 'defence mechanisms' and 'transcription'. Differentially expressed genes are dispersed throughout the chromosome, with the exception of the symbiosis island, where most genes remain unchanged. A significant number of transcriptional regulators and ABC transporter genes are overexpressed. No overexpression of genes typically associated to acid tolerance in rhizobia, such as act and exo genes, was detected. Overall, this study suggests a transcriptional response to acidic shock of M. loti distinct from other rhizobia. Additional studies are in course to explore the role of some of the highly overexpressed genes and to further elucidate the molecular bases of acid stress response.