After food, fossil fuel is humanity's most important source of energy. Sulfur oxides are produced by the oxidation of the available sulfur in the fuel. Biodesulfurization (BDS) could be an alternative technology to hydro-desulfurization (HDS) to remove sulfur from the recalcitrant organic compounds dissolved in crude oil fractions. It can be seen that all carbon nanotubes (CNTs) exhibited excellent catalytic performance for dibenzothiophene (DBT) oxidation when using molecular oxygen. In this study, chemical modification of Multiple Wall Carbon Nanotubes (MWCNTs) via oxidation followed by side wall functionalization using polyethylene glycol (PEG) was performed to improve the solubility of MWCNTs in aqueous solution. TEM, SEM, FT-IR spectra and Raman spectra were done for characterization of modified MWCNTs. Solubility of the modified MWCNTs studied using different solvents; deionized water, ethanol, and dimethyl sulfoxide (DMSO). Biodesulfurization capability investigated for Rodococcus erythropolis IGTS8 and Gordona rubropertinctus PTCC 1604 of DBT as sole sulfur source in basal salts medium. The results indicated in the presence of carbon nanotubes growth rate of R. erythropolis IGTS8 around 8% increases and G. rubropertinctus PTCC 1604 5% reduction was observed after 96 h. Gibb's assay results in the presence of carbon nanotubes showed desulfurization activity of R. erythropolis IGTS8 an increase of about 12% and for G. rubropertinctus PTCC 1604 was estimated about 15%.