Mercury (Hg) methylation is mainly a microbial process mediated by anaerobes. The continued study of Pseudomonas putida (P. putida) strain TGRB4 genome was inspired by the fact that it can transform Hg into the highly toxic methylmercury (MeHg) under aerobic conditions. P. putida strain TGRB4 is a Gram-negative rod-shaped Gamma-proteobacterium (gamma-proteobacterium), isolated from the soil in a typical water level fluctuation zone (WLFZ) of the Three Gorges Reservoir (TGR), which suffered from seasonally water level alternations every year. Draft genome assembly of P. putida strain TGRB4 is presented here, which was sequenced using Illumina Hiseq and PacBio single-molecule real-time (SMRT) platforms. Its genome harbors a total of 5504 genes and a G + C content of 62.6%. We further identified the enzymes related to Hg methylation, and found two well-known methyltransferase, including 5-methyl-tetrahydrofolate (5-methyl-THF) and S-adenosylmethionine (AdoMet), were annotated in the genome of P. putida strain TGRB4. This genome information could be treated as a research material to further study the Hg methylation mechanisms under aerobic environment.