Aims A structural and functional study has been carried out in the rice production area of the Guadalquivir marshes in southern Spain aiming to increase knowledge of rice rhizosphere structure and function for further application on integrated management practices. Methods and Results Rhizosphere bacterial structure (analysis of 16S rRNA partial sequences from total soil DNA), metabolic diversity (analysed by Biolog FF for fungal community and GN for microbial community) and a screening for putative plant growth-promoting rhizobacteria (PGPR) to identify potential isolates for development of local biofertilizers, and biodiversity of culturable micro-organisms (analysis of 16S rRNA partial sequences) from four areas differing in salinity and Magnaporthe oryzae incidence in two moments of the crop cycle were studied. Results indicate that the dominant taxon in libraries from the four areas was Proteobacteria. Metabolic diversity was higher in areas affected only by salinity or incidence of Magnaporthe than in the control or area affected by both stresses. It seems that rice plants selected, in their rhizosphere, micro-organisms able to affect plant hormonal balance under all conditions, and this activity relied in different bacterial genera depending on the environmental stress. Conclusions Bacterial genera for each stress, as well as generalist strains, were found present in all the studied areas. Potential molecular markers and taxonomic markers (Sphingobacteria for salt and Thermococci for Magnaporthe) of the different stress situations have been highlighted, and Class Verrucomicrobiae could be a marker for nonstressed areas. In addition, putative PGPR strains isolated in this study could be used as biofertilizers. Significance and Impact of the Study Rice paddies are great ecologically important ecosystems. The results are very relevant as they may be included in the process of rice production, improving crop conditions with less environmental impact.