Anaerobic oxidation of ammonium (anammox) is recognized as an important process for nitrogen (N) cycling, yet its role in agricultural ecosystems, which are intensively fertilized, remains unclear. In this study, we investigated the presence, activity, functional gene abundance and role of anammox bacteria in rhizosphere and non-rhizosphere paddy soils using catalyzed reporter deposition-fluorescence in situ hybridization, isotope-tracing technique, quantitative PCR assay and 16S rRNA gene clone libraries. Results showed that rhizosphere anammox contributed to 31-41% N2 production with activities of 0.33-0.64 nmol N2 g(-1) soil h(-1), whereas the non-rhizosphere anammox bacteria contributed to only 2-3% N2 production with lower activities of 0.08-0.26 nmol N2 g(-1) soil h(-1). Higher anammox bacterial cells were observed (0.75-1.4 × 10(7) copies g(-1) soil) in the rhizosphere, which were twofold higher compared with the non-rhizosphere soil (3.7-5.9 × 10(6) copies g(-1) soil). Phylogenetic analysis of the anammox bacterial 16S rRNA genes indicated that two genera of 'Candidatus Kuenenia' and 'Candidatus Brocadia' and the family of Planctomycetaceae were identified. We suggest the rhizosphere provides a favorable niche for anammox bacteria, which are important to N cycling, but were previously largely overlooked.