Use of an induced blanket reactor (IBR) to break down organic matter into methane is a financially attractive method to reduce the environmental impact of animal or industrial waste. In order to better understand the biological processes involved with the conversion of waste to biogas by an IBR, it is necessary to gain a better understanding of the microorganisms and their roles in the reactor. Molecular techniques based on the isolation of 16S rDNA were used in order to avoid the limitations posed by conventional culture-based techniques. Total DNA was extracted and amplified using universal primers specific to eubacteria and archaea with the purpose of identifying the dominant microorganisms in the IBR. The amplified DNA was separated based on its sequence composition by denaturing gradient gel electrophoresis (DGGE). Several bands were then excised, cloned, and sequenced, in order to characterize the phylogenetic affiliation of many of the microorganisms and create a useful molecular fingerprint. By using this approach, close relatives of several microorganisms that are typical in anaerobic digestion have been identified, including species of Clostridium, Flavobacterium, Bacteroides, Spirochaeta, Methanobrevibacter, and Methanosarcina. Several species were also identified whose role in the reactor is not completely understood, consisting of relatives of Dehalococcoides, Planctomyces, Aequorivita, and Sedimentibacter species. The information obtained in this project may enable refinements that promote desirable reactions and enhance reactor efficiency.