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Depending on season, mixed wastewater can show great deviations in terms of the influent ratios of tannery and seafood-wastewater. Increases in the ratio of tannery wastewater in influent water also result in increases in the concentration of chromium, which decreases the ratio of BOD/T-N so that the removal efficiency of organic and nitrogen pollutants in biological wastewater treatment deteriorates. No substantial differences occur in the ratios of Eubacteria/total bacteria as the ratio between tannery wastewater and seafood wastewater changes in the influent water. In contrast, the cell numbers and activities of Eubacteria and total bacteria significantly decline with increasing ratios of tannery wastewater in the influent water. Stable removal of organic and nitrogen pollutants by biological wastewater treatments leads to dominance of Proteobacteria groups in all biological treatment basins. In aeration and oxic basins, γ-Proteobacteria account for approximately 21% of the Eubacteria groups, at 1.9×109~ 2.0×109 cells/mL, while in an anoxic basin, β-Proteobacteria account for approximately 19% of the Eubacteria groups, at 1.3×109 cells/mL. However, a substantial decline in dominance of approximately 11% occurs for γ-Proteobacteria in aeration and oxic basins and about 1% for β-Proteobacteria in an anoxic basin. Mixed wastewater that undergoes extensive property changes of the influent water shows an efficiency of biological treatment that is greatly influenced by the ratio of dominant Proteobacteria groups.