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Microbial communities in a coastal aquifer in the Zhuhai region of southern China were investigated by culture-independent molecular approaches. Four 16S rRNA gene libraries of three groundwater, samples from varied depths and one seawater sample were constructed and analysed by the amplified ribosomal DNA restriction analysis technique (ARDRA). The phylogenetic analysis indicated that the 16S rDNA of clones presenting dominant ARDRA patterns were most similar to Proteobacteria, Bacteroidetes, Actinobacteria,Planctomycetes, and candidate divisions OPx (such as 0P3, 0P8, and OP11). In samples extracted from wells of 5-, 20-, and 35-m depth (i.e., D1, 05, and D6) Proteobacteria made up 32.3, 34.3, and 46.7% of the microbial communities, respectively. The same samples from Dl, D5, and D6 also consisted of 5.0, 11.2, and 6.5% Bacteroidetes and 5.4, 6.6, and 7.8% Actinobacteria, respectively. In contrast, the seawater clone library had a predominant number of Proteobacteria (32.8%), while Bacteroidetes and Planctomycetes both accounted for 9.3%. Total microbial diversity remained relatively constant over the top layer to a depth of approximately 35 m, significant community vertical and horizontal (seawater-groundwater) shifts were observed for certain bacterial populations. [ABSTRACT FROM AUTHOR]