Aims: This study aimed to characterize microbial community dynamics in aerated cow manure slurry at different aeration intensities. Methods and Results: Batch aerobic treatments were set up in 5-l jar fermentor, each containing 3 l of manure slurry; the slurries were subjected to low, medium and high (50, 150 and 250 ml min(-1), respectively) aeration for 9 days. Microbial community composition was determined using terminal restriction fragment length polymorphism and a clone library targeting 16S rRNA genes. High and medium aeration accelerated organic carbon degradation in parallel with the degree of aeration intensity; however, 90% of the initial total organic carbon was retained during low-aeration treatment. During the active stages of organic carbon decomposition, clones belonging to the class Bacilli accumulated. Moreover, Bacilli accumulation occurred earlier under high aeration than under medium aeration. Conclusions: Organic matter degradation was mainly governed by a common microbial assemblage consisting of many lineages belonging to the class Bacilli. The timing of community development differed depending on aeration intensity. Significance and Impact of the Study: This study reports on changes in several environmentally important parameters and the principal microbial assemblage during the pollution-reducing phase of cattle manure aeration treatment.