The bacterial community structure in a biological reactor fed influent from a wastewater treatment system was investigated by denaturing gradient gel electrophoresis (DGGE) and in situ hybridization. Sludges were collected from three biological reactors (aerobic, oxic, and anoxic tanks) at the M wastewater treatment facility (WTF). The influent of the MWTF consisted of mixed tannery wastewater (40~65%) and seafood wastewater (35~60%). The treatment processes resulted in a removal efficiency for BOD (biochemical oxygen demand) and COD (chemical oxygen demand) of 83.6~98.2% and 72.8~84.6%, respectively for tannery wastewater than for seafood wastewater resulted in greater survival of biomass in the biological reactors and a higher removal of BOD, COD, and T-N of about 8~18%. In contrast, addition of greater amounts of seafood wastewater decreased the amount of biomass in the bioreactors due to the increasing concentration of chromium from that wastewater and it also. The dominant bacterial species during the high seafood wastewater input period were Burkholderia cepacia (JX901049) and an uncultured bacterium (JF247555), while Pseudomonas geniculata (HQ256559) was dominant during the high tannery wastewater input period. Flavobacteriumsp. BF.107 (FM173271) and Hyphomicrobium zavarzinii (Y14306) were dominant under anoxic conditions.