The aim of this research was to identify key microorganisms for thermophilic (55 °C) anaerobic digestion of thin stillage derived from hydrolysis and ethanol fermentation of energy cane in a conventional stirred tank reactor with a 10-day hydraulic retention time. Efficient thermophilic anaerobic digestion with a specific methane production of 0.43 Lmethane/gtCOD used/d and biogas containing around 56% methane was accomplished. Due to an overnight temperature perturbation the specific methane production decreased to 0.16 Lmethane/gtCOD used/d. Analysis of the microbial community showed the importance of methanogenic Archaea belonging to Methanosarcina and Methanothermobacter as well as syntrophic Bacteria related to Thermacetogenium, Tepidanaerobacter and Anaerobaculum. This indicates that retention of biomass maintaining syntrophy and methanogenesis more efficiently may be useful for thermophilic anaerobic digestion of thin stillage derived from the production of energy cane ethanol.