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Objective To compare the bacterioplankton communities in streams exposed to pollution of different types. Methods The bacterioplankton communities in three selected heavily polluted streams were investigated by using terminal-restriction fragment length polymorphism (T-RFLP) analysis in combination with 16S rRNA gene clone library analysis. Results Both T-RFLP and 16S rRNA gene clone library revealed a great difference in bacterioplankton community composition in the different streams. Conclusion This work might provide some new insights into bioremediation of heavily polluted streams.