Microbial communities involved in biogas production from wheat straw as the sole substrate were investigated. Anaerobic digestion was carried out within an up-flow anaerobic solid-state (UASS) reactor connected to an anaerobic filter (AF) by liquor recirculation. Two lab-scale reactor systems were operated simultaneously at 37 °C and 55 °C. The UASS reactors were fed at a fixed organic loading rate of 2.5 g L(-1) d(-1), based on volatile solids. Molecular genetic analyses of the bacterial and archaeal communities within the UASS reactors (digestate and effluent liquor) and the AFs (biofilm carrier and effluent liquor) were conducted under steady-state conditions. The thermophilic UASS reactor had a considerably higher biogas and methane yield in comparison to the mesophilic UASS, while the mesophilic AF was slightly more productive than the thermophilic AF. When the thermophilic and mesophilic community structures were compared, the thermophilic system was characterized by a higher Firmicutes to Bacteroidetes ratio, as revealed by 16S rRNA gene (rrs) sequence analysis. The composition of the archaeal communities was phase-separated under thermophilic conditions, but rather stage-specific under mesophilic conditions. Family- and order-specific real-time PCR of methanogenic Archaea supported the taxonomic distribution obtained by rrs sequence analysis. The higher anaerobic digestion efficiency of the thermophilic compared to the mesophilic UASS reactor was accompanied by a high abundance of Firmicutes and Methanosarcina sp. in the thermophilic UASS biofilm.