Biomanipulation is reliable method for treating volatile organic compounds (VOCs) in polluted air. The performances of two biofilters in the removal of toluene vapors from air stream were compared. Two identical biofilters designed in parallel configuration were operated in lab-scale for 20 days; one of them was filled by sterilized media (compost and wood charcoal 2:1 v/v) and another was filled by the same media inoculated with Pseudomonas putida PTCC 1694, as a native strain. Moreover, batch tests were performed to determine the biodegradation rate of toluene. The results showed that, in comparison with the sterilized BF (89% vs 58%), the inoculated BF could effectively eliminate toluene from air stream. The pressure drop across the inoculated BF and the sterilized BF were 0.66±0.28 and 0.47±0.27 mm water respectively. The batch test results showed that loss of toluene in the control bottles was greater than the blanks. Based on the experimental results, inoculated BFs can effectively treat toluene vapors from gaseous streams.