Changes in methanogenic archaea were investigated in pilot-scale experiments during one- and two-stage mesophilic anaerobic digestion (AD) of food waste. Methane yields were 379.7±75.3 liters of methane per kg of volatile solids [L-CH4 (kg-VS)−1] added to the system, during one-stage operation, and 446±922 L-CH4 (kg-VS)−1 added during two-stage operation. Populations of methanogenic archaea were monitored quantitatively by targeting the functional gene for methyl-coenzyme-M reductase (mcrA) using real-time quantitative polymerase chain reaction techniques. During one-stage operation, mean mcrA gene concentrations were 2.48×109±2.7×109 copies ml−1. Two-stage operation yielded mean mcrA gene concentrations of 9.85×108±8.2×108 copies ml−1 in the fermentation and 1.76×1010±8.5×109 copies ml−1 in the methanogenesis reactors, respectively. Diversity of archaea in the methanogenic reactors was investigated by denaturing gradient gel electrophoresis targeting the V3 region of 16S rRNA of archaea. The Shannon index (H) was 2.98 for one-stage operation and 7.29 for two-stage operation, suggesting greater archaeal diversity in the two-stage AD. The fivefold increase in methanogenic archaea populations during the two-stage operation, as indicated by mcrA gene concentration, corresponded to an increase in methane production rates. While the diversity may also be related to the stability of the microbial bioprocesses and improved methane production rates, the correlation between diversity and production rates should be studied further.