The 99% of all microorganisms in naturecannot be isolated by standard culture methods without conspicuous external characters to classify them morphologically. In addition, classification based on physiological or biochemical features are often fuzzy. Molecular techniques are used for uncultured microorganisms to explore the diversity of microbial communities and novel resources without the need of cultivation. DNA dynamics and cloning of PCR products obtained from environmental DNA is now routinely used to identify microbial populations in microbial ecology. For practical reasons the approach is not suited to study the complex dynamics of microbial communities in environment. Genetic fingerprinting techniques are better tools, which give complement for the traditional microbiological methods. The methods are rapid and relatively easy to perform, and they allow the simultaneous analysis of multiple samples, which makes it possible to compare the genetic diversity of microbial communities from different habitats, or to study the behaviour of individual communities over time.