Technical Abstract: Swine slurry is stored in pits beneath confinement buildings or in adjacent lagoons. This slurry is a valuable resource for crop fertilization and soil conditioning, but may also be a source of unpleasant odors. Microorganisms are crucial to all of the important processes that occur in anaerobic storage systems. Therefore, understanding more about how the microbial community functions should aid in developing better strategies for management and use of stored slurries. In this study, molecular analyses were used to track changes in the microbial community of swine slurry from a 0.4 ha anaerobic lagoon over a period of one year and at four depths within the lagoon. The concentration and diversity of Bacteroides sp. was seasonal (as much as 90% decrease between March and June at all depths). Hespellia sp. and other clostridial species, on the other hand, were endemic in the slurry, present at all depths and high concentrations throughout the year. Results suggest that there were seasonal effects on the microbial community in the swine lagoon, while the effect of depth was not as pronounced. Seasonal changes in the microbial community in stored wastes may be (directly or indirectly) correlated with changes in malodor emissions from lagoons.