<p>Wetlands are the largest natural source of methane (CH₄), and trees as well as soils can be CH₄ sources. CH₄ emissions from dead trees are poorly understood. We examined stem CH₄ emissions targeting trees in different stages, namely, three living, four recently deceased and three old dead Japanese cypresses (<i>Chamaecyparis obtusa</i>) by the dynamic closed chamber method. We aimed to identify the differences in stem CH₄ emissions among trees in three categories and their impacts on the CH₄ budget of wetlands and to examine the factors controlling stem CH₄ fluxes. Stem CH₄ fluxes showed seasonal variation in all categories, and CH₄ emissions from recently deceased trees dropped rapidly since the measurement started. Recently deceased trees displaying the highest CH₄ emissions followed by old dead trees, while the lowest emissions were observed for living trees. In an incubation experiment, CH₄ production was confirmed from all dead trees but not significant production from living trees. Stem CH₄ emissions from old dead trees were greater at lower positions, and seasonal variations were significantly correlated with soil CH₄ emissions, which supported the degassing of belowground CH₄ through trees. On the other hand, stem CH₄ emissions from recently deceased trees did not show a consistent height dependency, suggesting the presence of additional sources. When compared per soil surface area, CH₄ emissions from dead cypress were smaller than those from wetland soils. However, CH₄ emissions from Japanese cypress can change when they die due to inundation and increased dead trees could be an additional CH₄ source.</p>