Variations in chemical parameters and bacterial populations in mangrove rhizosphere samples were noted for different sites. The C, N, P and K contents as well as pH, EC and salinity showed variation between sites. Significant differences in soil properties were also found in sampling sites. Two types of soil were noted among sites. Guesthouse had significantly higher organic matter and nutrient content (N) than other three sites suggesting that human discharges, litter deposition and surface runoff were major nutrient inputs. This contaminated site was located at the landward edges. Positive correlations between organic matter, N, P and K contents were found suggesting that these nutrients were from similar input sources. Effects of sampling sites on microbial diversity were also analyzed via SSCP. Porteresia coarctata and Rhizophora mucronata did not show any variation in the banding patterns among replicates sampled in short distance within site. But Sonneratia apetala showed variation among replicates sampled in distance within site. A significant variation was noted in the SSCP profile among replicates between sites. The majority of dominant SSCP band sequences were related to bacterial genera of root and root-free soil environments, namely Bacillus, Planococcus, Planomicrobium, low G+C Gram-positive bacterium, glacial ice bacterium and unidentified bacteria. In the analysis of 16S rRNA sequences, members belonging to the phylum Firmicutes dominated the sequence collection. The phylogenetic analysis of 16S rRNA gene sequences showed close relationships to a wide range of clones or bacterial species of phylum Firmicutes and unidentified bacteria.