The microbial community structures of two mesophilic anaerobic chemostats, one fed with glucose, the other with starch as sole carbon sources, were studied at various dilution rates (0.05–0.25 d for glucose and 0.025–0.1 d for starch) during two years continuous operation. In the glucose-fed chemostat, the aceticlastic methanogen spp. and hydrogenotrophic methanogen spp. predominated at low dilution rates, whereas spp. and the hydrogenotrophic spp. predominated together when dilution rates were greater than 0.1 d . Bacteria affiliated with the phyla Bacteroidetes, Spirochaetes, and Actinobacteria predominated at dilution rates of 0.05, 0.1, and 0.15 d , respectively, while Firmicutes predominated at higher dilution rates (0.2 and 0.25 d ). In the starch-fed chemostat, the aceticlastic and hydrogenotrophic methanogens coexisted at all dilution rates. Although bacteria belonging to only two phyla were mainly responsible for starch degradation (Spirochaetes at the dilution rate of 0.08 d and Firmicutes at other dilution rates), different bacterial genera were identified at different dilution rates. With the exception of Archaea in the glucose-fed chemostat, the band patterns revealed by denaturing gradient gel electrophoresis (DGGE) of the microbial communities in the two chemostats displayed marked changes during long-term operation at a constant dilution rate. The bacterial community changed with changes in the dilution rate, and was erratic during long-term operation in both glucose-fed and starch-fed chemostats.