Very few studies have conducted long-term observations of methane (CH4) flux over forest canopies. In this study, we continuously measured CH4 fluxes over an evergreen coniferous (Japanese cypress) forest canopy throughout 1 year, using a micrometeorological relaxed eddy accumulation (REA) system with tuneable diode laser spectroscopy (TDLS) detection. The Japanese cypress forest, which is a common forest type in warm-temperate Asian monsoon regions with a wet summer, switched seasonally between a sink and source of CH4 probably because of competition by methanogens and methanotrophs, which are both influenced by soil conditions (e.g., soil temperature and soil moisture). At hourly to daily timescales, the CH4 fluxes were sensitive to rainfall, probably because CH4 emission increased and/or absorption decreased during and after rainfall. The observed canopy-scale fluxes showed complex behaviours beyond those expected from previous plot-scale measurements and the CH4 fluxes changed from sink to source and vice versa.