Ten mesophilic full-scale anaerobic digesters treating food wastewater (FW-digesters) or sewage sludge (SL-digesters) were monitored for 1 year to investigate: (1) microbial communities underpinning FW-digesters and SL-digesters, (2) the effects of total ammonia-nitrogen concentration [TAN] and Na+ concentration [Na+] on variations of these communities. [TAN] and [Na+] in the digester varied among digesters: 1.7-6.5 g TAN/L and 1.0-3.6 g Na+/L for the FW-digesters, and 0.1-2.2 g TAN/L and 0.1-1.2 g Na+/L for the SL-digesters; [TAN] negatively correlated with the process efficiency of the FW-digesters. Microbial communities were less diverse in the FW-digesters than in the SL-digesters. The FW- and SL-digesters formed very distinct microbial community structures; [TAN] and [Na+] in the digester were the critical factors shaping these structures. Immigrant bacteria from influent sludge significantly influence the bacterial communities of the SL-digesters. Methanoculleus might be tolerant to high ammonia in AD of such organic wastewater.