The development of molecular biological techniques has allowed us to study microbial diversity at a different level, the genetic level. Microbes are grouped according to similar- ities in their genes, which also reflect their evolutionary relationship [2]. T h e most powerful approach to explore microbial diversity in natural samples is cloning and sequencing of 16S ribosomal RNA (rRNA) encoding genes [3°]. By using this approach we now know that microbial diversity is much greater than previously anticipated, and that culture techniques are insufficient for exploring this enormous reservoir of hidden diversity. Although important, exploration of microbial diversity is just one aspect in micro- bial ecology; the study of successional population changes in microbial communities is another, and for this purpose the cloning approach is not well suited, simply because it is too laborious, time consuming, and expensive. Hybridization techniques using specific oligonucleotide probes are more appropriate for studying population dynamics, but probes rely on sequence data and are either too specific, targeting only one particular population, or too general, overlooking closely related but ecologically different populations. So to determine the diversity of different microorganisms in natur- al ecosystems, and to monitor microbial community behavior over time, other approaches are needed. One such approach is genetic fingerprinting of complex microbial communities.