Microbial community structure of the DHS reactor was investigated by 16S rRNA and functional gene targeted clone-sequence analysis. A known toluene degrading microorganisms of Pseudomonas species were existed in each sampling point. Especially, at the bottom of the DHS reactor, toluene-degrading microorganisms were dominantly detected. Quantitative real-time PCR targeting the functional genes of toluene degradation in a sponge of bottom of DHS reactor revealed that copy genes by tmoA targeted primer set, which encoding the part of toluene-4-monooxygenase, was mostly existed in outside of the sponge. Copy genes by tbmD targeted primer set, which encoding the part of toluene/benzene-2-monooxygenase, was existed in the every part of the sponge. Copy genes by todC targeted primer set, which encoding the part of xylene dioxygenase, was not only existed in outside of the sponge, but also existed in inside of the sponge. Based on these results, toluene degradation was occurred in both of outside and inside of the sponge.