Recent developments in microbial techniques (such as PCR, GE, FISH) have allowed researchers to detect, identify and quantify microorganisms without the limitation of culture-dependent methods. This has given both engineers and scientists a more fundamental understanding about systems containing microorganisms. These techniques can be used to monitor bacteria in wastewater treatment systems, soil and sea, industrial fermentation, food technology, and improve floccability, etc. However, despite these techniques being readily available and relatively cheap, they are not widely used by engineers. Hence, the aim of this paper is to introduce these techniques, and their applications, to chemical engineers. Two different studies related to industrial wastewater treatment, but applicable to general microorganism systems, will be presented: (1) microbial stability of pure cultures, and (2) bioreactor population shifts during alternating operational conditions. In (1), two bioreactors, inoculated with two different pure cultures, (A) Xanthobacter aut GJ10 and (B) Bulkholderia sp JS150, degrading 1,2-dichloroethane (DCE) and monochlorobenzene (MCB), respectively, were followed over time (Emanuelsson et al., 2005). Specific and universal 16S rRNA oligonucleotide probes were used to identify the bacteria. It was found that bioreactor (A) remained pure for 290 days, whereas bioreactor (B) became contaminated within one week. The difference in behaviour is attributed to the pathway required to degrade DCE. In (2), the stability of a bacterial strain, which was isolated on the basis of its capability to degrade 2-fluorobenzoate from contaminated soil, in three different, up-flow fixed bed reactors operated under shock loads and starvation periods, was followed by denaturing gradient gel electrophoresis (DGGE) (Emanuelsson et al., 2006). All bioreactors were rapidly colonised by different bacteria; however, the communities remained fairly stable over time, and shifts in bacterial populations were mainly found during the starvation periods.