The complete nucleotide sequence of the genome of the 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%. No plasmids were detected. The chromosome contains 8,317 potential protein-coding genes, one set of rRNA genes, and 50 tRNA genes. Fifty-two percent of the potential protein genes show sequence similarity to known genes, 30% to hypothetical genes, and 18% to no known genes. Thirty-four percent of the genes show significant sequence similarity to those of *Mesorhizobium loti* and *Sinorhizobium meliloti*, while 23% are unique to *B. japonicum*. A presumptive symbiosis island of 681 kb was identified, containing 655 putative protein-coding genes, including those related to symbiotic nitrogen fixation and DNA transmission. Six hundred sixty-five transposase genes were identified, with 100 located in the symbiosis island. DNA segments of 4 to 97 kb were found inserted into tRNA genes at 14 locations, indicating partial duplication and suggesting genome plasticity due to complex rearrangements. The study provides insights into the genetic mechanisms underlying the symbiotic nitrogen fixation process in *B. japonicum*.The complete nucleotide sequence of the genome of the 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%. No plasmids were detected. The chromosome contains 8,317 potential protein-coding genes, one set of rRNA genes, and 50 tRNA genes. Fifty-two percent of the potential protein genes show sequence similarity to known genes, 30% to hypothetical genes, and 18% to no known genes. Thirty-four percent of the genes show significant sequence similarity to those of *Mesorhizobium loti* and *Sinorhizobium meliloti*, while 23% are unique to *B. japonicum*. A presumptive symbiosis island of 681 kb was identified, containing 655 putative protein-coding genes, including those related to symbiotic nitrogen fixation and DNA transmission. Six hundred sixty-five transposase genes were identified, with 100 located in the symbiosis island. DNA segments of 4 to 97 kb were found inserted into tRNA genes at 14 locations, indicating partial duplication and suggesting genome plasticity due to complex rearrangements. The study provides insights into the genetic mechanisms underlying the symbiotic nitrogen fixation process in *B. japonicum*.