AbstractSludge from the wastewater treatment plants (WWTPs) has been recognized as a reservoir of antibiotic resistance genes (ARGs). Free ammonia (FA, i.e. NH3-N) pretreatment has been demonstrated to be able to enhance anaerobic digestion, which is a widely used method for sludge treatment. However, the effect of combined FA pretreatment and anaerobic digestion on the fate of ARGs is still unknown. This study demonstrated for the first time that combined FA pretreatment (420 mg NH3-N/L for 24 h) and anaerobic digestion could reduce the abundances of the tested ARGs by 0.06 log10 gene copies/g TS (total solids) compared with the anaerobic digestion alone. Specifically, the experimental results showed that combined FA pretreatment and anaerobic digestion reduced the abundances of aac(6’)-Ib-cr, blaTEM, sul2, tetA, tetB and tetX by 0.07, 0.37, 0.09, 0.32, 0.24 and 0.59 log10 gene copies/g TS compared with anaerobic digestion alone. In contrast, combined FA pretreatment and anaerobic digestion slightly increased the abundance of tetG by 0.05 log10 gene copies/g TS compared with anaerobic digestion alone. In addition, FA pretreatment did not significantly affect the abundance of sul1 and tetM during anaerobic digestion. This study revealed that FA pretreatment for anaerobic digestion could potentially reduce the spread of antibiotic resistance from the sludge to soil (while agriculture reuse is used as the sludge disposal method), thereby protecting the environment and human health.