Groundwater at many military factory, munition storage and maneuver sites is contaminated by explosives chemicals that were released into the subsurface. The 2,4,6-trinitrotoluene (TNT) is among the most common explosive pollutants. In this study, two TNT-degrading strains, isolated from TNT-contaminated soils and wastewater sludge, were applied for TNT biodegradation. Based on the 16S rDNA sequence analyses, these two bacterial strains were identified as Achromobacter sp. and Klebsiella sp. via biochemical and DNA analyses. Microcosm study was conducted to evaluate the feasibility and efficiency of TNT biodegradation under aerobic conditions. Results indicate that TNT degradation by-products were detected in microcosms (inoculated with Achromobacter sp. and Klebsiella sp.) with cane molasses addition. Klebsiella sp. and Achromobacter sp. used TNT as the nitrogen source and caused completely removal of TNT. Two possible TNT biodegradation routes could be derived: (1) part of the TNT was transformed to nitrotoluene then transformed to nitrobenzene followed by the nitro substitute process, and trinitrobenzene, dinitrobenzene, and nitrobenzene were detected; and (2) TNT was transformed via the nitro substitute mechanism, and dinitrotoluene followed by nitrotoluene isomers were detected. The initial TNT degradation involved the reduction or removal of the nitro substitute to an amino derivative or free nitrite. Results show that the second route was the dominant TNT biodegradation pathway. The produced by-products were also degraded without significant accumulation during the degradation process. These findings would be helpful in designing a practical system inoculated with isolated TNT degradation strains for the treatment of TNT-contained groundwater.