An increasing amount of attention has been given to antimicrobial resistance in the environment because of its substantial threat to human health. The effluent from municipal wastewater treatment plants has been regarded as one of the important sources for the spread of antibiotic resistance genes (ARGs). However, conventional disinfection techniques fail to effectively remove ARGs from effluents. In this work, in situ synthesized hydrated manganese oxide (HMO) coupled with permanganate was applied for the first time in ARG removal from the effluent of wastewater treatment plants. The results show that five ARGs (sulI, sulII, tetQ, tetO, and tetW) as well as the intI1 and 16S rRNA genes had removal efficiencies of 2.46-4.23 logs, which were significantly higher than those obtained by using these reagents individually. This implied that there was a synergistic effect between permanganate and HMO toward the removal of ARGs. Moreover, the contributions of HMO coagulation and permanganate oxidation to ARG removal were semiquantitatively studied, which demonstrated that destruction of the microbial cells by oxidation and removal of the extracellular ARGs released by coagulation were the two main processes in this system. The results of this study provide an alternative method for ARG removal from the effluent of wastewater treatment plants with high efficiencies to control the spreading of ARGs.