Microbial population size, community structure, and diversity, and the correlations of these characteristics with process variables were investigated in samples taken seasonally over two years from a full-scale thermophilic anaerobic digester treating food waste-recycling wastewater (FRW). The organic component of the FRW consisted of carbohydrate (35% of volatile solids), protein (34%) and lipid (30%). The chemical oxygen demand (COD) removal efficiency of the anaerobic digestion (AD) system negatively correlated with Na+ (2.9-7.7 g/L) and lipid (33-22.8 g/L) concentrations, which varied significantly over the two years. Tepidanaerobacter, Anaerobaculum, Defluviitoga, Keratinibaculum, Gelria, Tepidimicrobium, Caldicoprobacter, Bacillus, and Syntrophaceticus were the major bacterial genera, and Methanoculleus and Methanobacterium were the major archaeal genera. Concentrations of Na+ and lipid in the digester were negatively correlated with total bacterial and archaeal populations determined by real-time quantitative PCR. These concentrations could also significantly affect the bacterial community structure (e.g., negative correlations with Gelria), but not archaeal community structure. Lipid concentration was negatively correlated with bacterial diversity, but was not correlated with archaeal diversity. Ammonia concentration in the digester (2.0-4.3 g N/L) had no significant correlation with COD removal or total bacterial/archaeal populations, but could significantly affect both bacterial and archaeal community structures, including syntrophic acetate-oxidizing bacteria and hydrogenotrophic methanogens. These results indicate that Na+, lipid and ammonia are among the key parameters that affect the process performance of a thermophilic AD system treating FRW and/or the microbial communities in it. (C) 2016 Elsevier B.V. All rights reserved.