Two large-scale municipal solid waste incinerators (MWIs) located in Taiwan were selected for conducting flue gas sampling to determine the chemical speciation of mercury by both USEPA Method 29 and Ontario Hydro Method (OHM). In addition, the emission characteristics and removal efficiencies of mercury were evaluated via isokinetic sampling of flue gas upstream and downstream of APCDs. Results indicated that the average removal efficiencies of Hg for MWI-A and MWI-B were 29.56 and 44.70%, respectively. In terms of mercury speciation by USEPA Method 29 and Ontario Hydro Method (OHM), oxidized mercury (Hg2+), in the flue gas was predominant at the inlet of APCD for both incinerators. Less than 30% of mercury in the flue gas existed in the elemental form (Hg0) at APCD inlet. Mercury emitted from the stack also predominated as a form of Hg2+ in MWI-A. Approximately 90% of total mercury emission from the stack existed in the form of Hg2+ for MWI-A. Due to the higher removal efficiency of soluble mercury (Hg2+) in wet scrubber, less total Hg was actually emitted from MWI-B than MWI-A. Regarding the removal efficiency of Hg0 in the flue gas, the APCDs of MWI-A (DSI + FF) had a higher removal efficiency than that of MWI-B (ESP + WS) possibly due to the reduction of Hg2+ which occurred in the wet scrubber.