The complete genome sequence of the nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110 was determined. The genome is a single circular chromosome of 9,105,828 bp with an average GC content of 64.1% and contains 8,317 potential protein-coding genes, one set of rRNA genes, and 50 tRNA genes. Approximately 52% of the protein-coding genes showed sequence similarity to known genes, while 30% were hypothetical and 18% had no apparent similarity. A 681-kb region, including a 410-kb symbiotic region previously identified, was identified as a potential symbiosis island. This region contains 655 putative protein-coding genes, including those involved in symbiotic nitrogen fixation and DNA transmission. The genome also contains 167 transposase genes and 104 insertion sequences, with 100 of the transposase genes located in the symbiosis island. DNA segments of 4 to 97 kb were inserted into tRNA genes, leading to partial duplication of the target tRNA genes. These observations suggest genome plasticity due to complex rearrangements such as horizontal transfer and insertion of various DNA elements, and homologous recombination. The genome of B. japonicum USDA110 was compared with those of Mesorhizobium loti and Sinorhizobium meliloti, revealing significant similarities and unique genes. The genome contains genes related to symbiotic nitrogen fixation, including those for nitrogenase, nitrogen fixation, and other essential processes. The genome also includes genes for flagella formation, chemotaxis, and other functions. The genome sequence is available in the RhizoBase database and DDBJ/GenBank/EMBL under accession number BA000040. This study provides insights into the genetic basis of symbiotic nitrogen fixation and the evolution of the genome of B. japonicum.The complete genome sequence of the nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110 was determined. The genome is a single circular chromosome of 9,105,828 bp with an average GC content of 64.1% and contains 8,317 potential protein-coding genes, one set of rRNA genes, and 50 tRNA genes. Approximately 52% of the protein-coding genes showed sequence similarity to known genes, while 30% were hypothetical and 18% had no apparent similarity. A 681-kb region, including a 410-kb symbiotic region previously identified, was identified as a potential symbiosis island. This region contains 655 putative protein-coding genes, including those involved in symbiotic nitrogen fixation and DNA transmission. The genome also contains 167 transposase genes and 104 insertion sequences, with 100 of the transposase genes located in the symbiosis island. DNA segments of 4 to 97 kb were inserted into tRNA genes, leading to partial duplication of the target tRNA genes. These observations suggest genome plasticity due to complex rearrangements such as horizontal transfer and insertion of various DNA elements, and homologous recombination. The genome of B. japonicum USDA110 was compared with those of Mesorhizobium loti and Sinorhizobium meliloti, revealing significant similarities and unique genes. The genome contains genes related to symbiotic nitrogen fixation, including those for nitrogenase, nitrogen fixation, and other essential processes. The genome also includes genes for flagella formation, chemotaxis, and other functions. The genome sequence is available in the RhizoBase database and DDBJ/GenBank/EMBL under accession number BA000040. This study provides insights into the genetic basis of symbiotic nitrogen fixation and the evolution of the genome of B. japonicum.