Technical Abstract: Skatole is one of the most malodorous compounds produced as a by-product of anaerobic degradation of animal waste materials. Little is known of the biochemistry involved in skatole production, the phylogeny of skatole-producing microorganisms or the conditions that favor their growth. These deficiencies hamper attempts to reduce skatole production. Our goals were to enrich for skatole-producers in swine lagoon slurry (SLS) and evaluate the resulting microbial community structure using denaturing gradient gel electrophoresis (DGGE) and 16S rDNA sequence analysis. Skatole producers were enriched by incubating dilutions of SLS with 100 µM indole-3-acetic acid (IAA). GC-MS was used to measure skatole production in the slurries after 0, 7 and 17 days incubation. Based on MPN analysis, skatole producers increased hundred fold (2-12 x 102 cells mL-1 on day 7 to 3-14 X 104 cells mL-1 on day 17) in SLS samples supplemented with IAA. Based on DGGE fingerprint patterns from triplicate samples taken from day 0, 7 and 17 treatments with high, mid or low levels of skatole production, changes in the SLS population occurred as skatole production increased. Samples producing high concentrations of skatole were distinct from those that produced no skatole. Based on analysis of DGGE band intensity and the corresponding 16S rDNA clone sequences, changes in the bacterial community fingerprints were associated with an increase in the low-GC gram positives and in the Bacteroides groups. Results from this study should provide valuable new information concerning the organisms responsible for production of this odorant, a necessary first step towards controlling skatole production.