The aim of this study was to monitor the changes in methanogenic community structures in an anaerobic digester (250 m(3) working volume) during start-up including prolonged starvation periods. Redundancy analysis was performed to investigate the correlations between environmental variables and microbial community structures. The anaerobic digester was operated for 591 days at alternating operating temperatures. In initial start-up period at stage I (35 degrees C), growth of various species of mesophilic aceti-clastic methanogens (AMs) and hydrogenotrophic methanogens (HMs) was observed. Methanobacteriales species survived better than other methanogens under long-term starvation conditions. In stage II (50 degrees C), HMs became dominant over AMs as the operating temperature changed from mesophilic to thermophilic due to increase of ammonia inhibition. In stage III (35 degrees C), only the Methanomicrobiales population significantly increased during 50 days of HRT while Methanobacteriales dominated over 15 days of HRT. The influent pH negatively correlated with all methanogenic populations especially in stage II. (C) 2013 Elsevier Ltd. All rights reserved.