We established a chemostat cultivation method for a mesophilic methanogenic consortium that could degrade long-chain fatty acids (LCFA) using a completely stirred tank reactor (CSTR) fed with synthetic wastewater containing oleic and palmitic acids as the carbon and energy sources. The critical dilution rate of the chemostat, in which most of the introduced LCFA were decomposed and mineralized, was 0.4 d(-1). The microbial community under steady-state condition at this dilution rate was analyzed by 16S rRNA gene sequencing. We detected the following major groups of methanogens within the archaeal community: the aceticlastic genera Methanosaeta and Methanosarcina and the hydrogenotrophic genus Methanospirillum. We also detected organisms that were closely related to fatty-acid oxidizing bacteria affiliated with the family Syntrophomonadaceae. However, bacteria belonging to the phyla Bacteroidetes and Spirochaetes, which are phylogenetically distant from known fatty-acid oxidizing bacteria, apparently predominated in the population, indicating that they play important roles in LCFA degradation within the chemostat.