The phylogenetic diversity of Bacteria and Archaea in water retrieved from a Dutch oil field and units of the associated oil-water separation site were determined using two culture-independent methods. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments was used to scan the microbial diversity in (1) the oil-water emulsion produced, (2) two different oil-water separator tanks, (3) a wash tank and (4) a water injector. Longer 16S rRNA gene fragments were amplified, cloned and sequenced to determine the diversity in more detail. One of the questions addressed was whether the detected microorganisms could serve as indicators for the environments from which they were retrieved. It was observed that the community found in the production water resembled those reported previously in oil reservoirs, indicating that these ecosystems harbor specific microbial communities. It was shown that changes, like a decrease in temperature, cause a distinctive shift in these communities. The addition of SO(3)(2-) to the wash tank as ammonium bisulphite, used in the oil industry to scavenge oxygen, resulted in a complete community change, giving rise to an unwanted sulphate-reducing community. The fact that these changes in the community can be linked to changes in their environment might indicate that these tools can be used for the monitoring of changing conditions in oil reservoirs upon, for example, water flooding.