We present the draft genome sequence of Bradyrhizobium sp. strain Ce-3, which produced exopolysaccharide (EPS) and oxidized methanol in the presence of Ce3+. The genome for strain Ce-3 was estimated at 7,608,996 bp and showed that the strain is closely related to Bradyrhizobium erythrophlei MT12 and Bradyrhizobium sp. strain C9.