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The microbial populations were investigated in two groundwater samples, GW-H and GW-S, which represented heavily and slightly polluted aquifers by a seaside landfill. The concentrations of dissolved redox-relevant species suggested that iron-reduction/sulfate-reduction and denitrification were major redox processes for GW-H and GW-S. The dominant microbial populations were determined using restriction fragment length polymorphism analyses of 16S rRNA gene clone libraries. These microbes were then further studied by sequencing and phylogenetic analyses. The results indicate an obvious variation of the dominant populations between the two samples. The coexistence of sequences related to denitrifiers, sulfur-reducers, and methanotrophic bacteria was found in the GW-S sample, and a sequence associated with a sulfate-reducer was also found in the GW-H sample using molecular analyses. These results suggest that the molecular approach may be an important supplement to other approaches in characterizing the redox processes in polluted aquifers.