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Abstract Biochar application can depress nitrification in paddy soils, but the microbiological mechanisms involved in this process are not clearly understood. This study was conducted to test the hypothesis that biochar may affect nitrification bacteria in paddy soils. Bacterial communities in a paddy soil with and without applications of biochar were compared in a field experiment. Results indicated that the total number of operational taxonomic units (OTUs) of bacteria was not significantly affected by biochar application (20 Mg rice husk biochar ha–1). However, the application of biochar significantly changed the structure of the bacterial community. In particular, the number of OTUs affiliated with Nitrospirae, a key bacterial phylum in nitrification, was significantly reduced, by 25%, by biochar application. The biochar‐induced reduction in Nitrospirae could be explained in part by interspecific competition with Firmicutes and Bacteroidetes phyla, which were significantly increased by application of biochar. The results of this study suggest that biochar may affect nitrification by changing levels of nitrification bacteria in paddy soils.