The applicability of a new molecular fingerprinting method (Single Strand Conformation Polymorphism) to study the microbial populations of anaerobic digestors was investigated. After extraction of total nucleic acids, the 16S rDNA and 16S rRNA molecules were amplified and the amplicons were separated by SSCP electrophoresis. Characteristic and complex peak patterns were obtained, where each peak could be correlated with the 16S rDNA sequence of one micro-organism. The rDNA peak patterns should consist of the most abundant sequences and thus would reflect the diversity of prominent species of different digestors. Ribosomal DNA patterns were compared to rRNA patterns and revealed the bacteria that were the most active metabolically. The SSCP method also revealed dynamic changes in the presence and activity of populations, following perturbations such as an acidic shock which caused an increase in activity of two species. After cloning the 16S rDNA, the species corresponding to the peaks of interest, such as the archaeal species, could be identified by screening the clones according to their SSCP patterns and sequencing the 16S rDNA.