BACKGROUND: The effect of molybdate on a microbial consortium of dry thermophilic anaerobic digestion (AD) from sulfate-containing municipal solid waste was studied. RESULTS: The study showed molybdate inhibition affecting hydrolysis, acidogenesis, and methanogenesis, but the main microbial populations in AD can sustain the molybdate load over a short period of time. Molybdate was not a bactericide for all members of the principal groups, only a few of them are affected. Although all the microbial populations decreased, the weakest groups were sulfate reducing bacteria (SRBs) and butyrate-utilising acetogens (BUAs) and the most resistant group was propionate-utilising acetogens (PUAs). Prior to using molybdate, the relative percentages were: Eubacteria:Archaea 80:20; acetogens 25% (BUAs 11% and PUAs 14%) and SRBs 17%. After molybdate addition the relative percentages were: Eubacteria:Archaea were 83:17, acetogens remained over 28% (BUAs 8% and PUAs 20%) and SRBs around 11%. The relation between acetate-utilising methanogens (AUMs) and hydrogen-utilising methanogens (HUMs) changed slightly from 55:45 to 53:47. CONCLUSION: All biochemical reactions in AD were inhibited and an increase in food: microorganism(F:M) ratio was observed. The microorganism's removal rates and growth inhibition rates are indicators of inhibitory effect in all analysed populations by inhibitor addition. (C) 2013 Society of Chemical Industry