The novel strain TF-2, isolated from a contaminated site and identified as Burkholderia stabilis, is able to degrade chlorobenzene via assimilation (51%-89%) and co-metabolism (98%-100%) for 60–200 mg/L chlorobenzene. Whole-genome sequencing experiments of strain TF-2 were carried out to reveal its global metabolism. Notably, 19 aromatic hydrocarbon dioxygenase genes and a gene cluster related to chlorobenzene metabolism were discovered in this strain. Moreover, the complete genome of strain TF-2 is composed of three circular chromosomes and two plasmids. The total length is 8.83 Mb, containing 8,807 protein coding genes, 18 rRNA genes and 69 tRNAs genes. Additionally, it contains 209 carbohydrate-active-enzyme-encoding genes, of which mainly 33.0% distributed in glycosyl transferases, 24.8% in carbohydrate esterases and 21.1% in auxiliary activities. Finally, the degradation pathway of chlorobenzene in TF-2 was proposed. The annotated complete genome sequence of TF-2 will provide genetic insights into the degradation of chlorobenzenes.