Methane is an important greenhouse gas, and the global warming potential of methane is about 20-30 folds greater than carbon dioxide on a per-molecule basis. Inland wetlands and freshwater aquatic systems (like lakes, rivers and reservoirs) are important sources of methane emissions. It is estimated that the annul flux of methane from inland wetlands is approximately 100-200 Tg, accounting for 30% of the global annual methane emissions. The annul fluxes of methane from lakes, rivers and reservoirs are estimated to be 8-48, 1.5-26.8 and 8.9-22.2 Tg, respectively. Microbial-mediated anaerobic oxidation of methane (AOM) plays an important role in reducing methane emissions form these ecosystems, which can greatly alleviate global warming. The anoxic conditions can develop easily in inland wetlands, lakes, rivers and reservoirs. In the meantime, these environments contain a great variety of electron acceptors. Such conditions provide an ideal environment for AOM. In recent years, there has been an increasing evidence showing the occurrence of AOM driven by different electron acceptors, including NO₂^-, NO₃^-, SO₄^2- and Fe(III) in inland wetlands and freshwater aquatic systems. The nitrite-dependent AOM is performed by the NC10 phylum bacteria, which can produce oxygen intracellularly from two NO molecules for methane oxidation and respiration. Under anoxic conditions, these bacteria can transcribe and express the entire biochemical pathway of aerobic methane oxidation catalyzed by particulate methane monooxygenase. The nitrate-dependent AOM is catalyzed by a new cluster of anaerobic methanotrophic archaea (ANME)-ANME-2d, which is capable of performing AOM through reverse methanogenesis coupling with the reduction of NO₃^- to NO₂^-. But these archaea cannot reduce the produced NO₂^- further to NO, N₂O or N₂. The ANME-2d also has the potential to use Fe(III), Mn(IV), Cr(VI) and SO₄^2- as electron acceptors for methane oxidation. It has been reported that the ANME-2d could oxidize methane solely and transfer electrons directly to metal compound. These archaea may also be involved in metal-dependent AOM together with metal-reducing bacteria. Similarly, the ANME-2d can conduct AOM couple to the conversion of SO₄^2- to S^2-, in collaboration with sulfate-reducing bacteria. Due to the presence of diverse electron acceptors in inland wetlands and freshwater aquatic systems, they may support a greater variety of AOM pathways. This work systematically reviewed the AOM pathways driven by different electron acceptors and the responsible microorganisms, and analyzed the importance and environmental regulation of these AOM pathways in reducing methane emissions from inland wetlands and freshwater aquatic systems. Further, the methods for molecular detection of anaerobic methanotrophs and the stable isotope technology for determination of the activity of anaerobic methane oxidation were summarized. Finally, some future research directions were suggested.