Microbial community in thermophilic contact oxidation process treating high strength organic wastewater with edible oil was analyzed by FISH, quinone profile, PCR-DGGE and sequencing of DGGE bands. Proteobacteria was abundant during mesophilic phases and Gram positive bacteria with low G+C content predominated during thermophilic phases. Constituents of the community under excellent and poor degradation were completely different even during thermophilic phases. Sequences from samples under excellent degradation implied that possible species which contributed good performance could be neighbors of known thermophilic Bacilli, such as Bacillus thermocloacae. The combination of the four methods can effectively and certainly analyze community from group to species level.