Aims: To study the diversity of thermophiles during thermophilic aerobic digestion (TAD) of agro-food waste slurries under conditions similar to full-scale processes. Methods and Results: Population diversity and development in TAD were studied by standard microbiological techniques and the processes monitored by standard fermentation procedures. Facultative thermophiles were identified as Bacillus coagulans and B. licheniformis, while obligate thermophiles were identified as B. stearothermophilus. They developed rapidly to peaks of 10(7) to 10(8) in <= 48 h. Stability of obligate thermophiles increased with process temperatures. Thermophiles were unstable at process pH above or below neutral, but developed rapidly at all aeration rates. Peak populations were higher in the median than at extremes of aeration rates. Obligate thermophiles were unstable at low aeration rates. Process self-heating was higher at lower than at higher aeration rate. Beyond 96 h most thermophiles were present as spores. Conclusions: Limited range of indigenous thermophiles drives TAD of slurry. They develop rapidly and are stable at most digestion conditions. Significance and Impact of the Study: Development and stability of thermophiles in TAD suggest that the process may be operated in a wide range of conditions; and even at short HRT in continuous processes without compromising efficiency.