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Methane (CH4) is one of the potent greenhouse gases emitted from municipal wastewater treatment plants. The characteristics of methane emission from municipal wastewater treatment plants (WWTPs) have attracted lots of concern from related researchers. The present work investigated the source of methanogens and methane emission properties from two WWTPs in Xi'an, and one is employed in an Orbal oxidation ditch, and the other is anaerobic/anoxic/oxic (A/A/O). The measurement of specific methanogenic activity (SMA) and coenzyme F420 concentration, together with Fluorescence in situ hybridization (FISH), was used to determine the amount and activity of methanogens in two WWTPs. Additionally, a combined activated sludge model was built and predicted the growth of methanogens and other key microorganisms in the sludge. The results showed that the average CH4 emission flux from the Orbal oxidation ditch (22.74 g CH4 /(m2·d)) was much higher than that from A/A/O (9.57 g CH4/(m2·d)). The methane emission factors in the Orbal oxidation ditch and A/A/O processes were 1.18 and 0.21 g CH4 /(m3 INF), respectively. These distinct methane emission characteristics between two WWTPs are mainly attributed to the higher activity and content of methanogens, as well as the discontinuous aeration in the Orbal oxidation ditch. Additionally, dissolved oxygen concentration, water temperature, and the presence of nitrate/nitrite were also important factors that influenced methane emission. The FISH analysis showed that Methanococcus was the dominant methanogen in both WWTPs. In addition, the combined model successfully simulated the growth of methanogens in WWTPs. Methanogens in WWTPs were mainly derived from the sewer system, and the cumulative effect led to an increase in the abundance of methanogens in activated sludge. The outcomes of this study provide new insights in the prediction and management of GHG emission from WWTPs. [ABSTRACT FROM AUTHOR]