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The objectives of this study were to clarify the effect of chemical fertilizer and manure application on methane (CH4) and nitrous oxide (N2O) emissions from intensively managed grassland on Andosols in Japan and to determine the controlling factors of the CH4 and N2O emissions. The emission factors (EF) for both fertilizer- and manure-induced N2O emissions were calculated. Three experimental plots were set up in five grasslands across four climatic regions in Japan: one plot for treatment with chemical fertilizer (fertilizer plot); another plot for treatment with cattle manure and chemical fertilizer (manure plot), and the final plot was not treated with chemical fertilizer or manure (control plot). The type of chemical fertilizer was ammonium-based fertilizer or a combination fertilizer of ammonium and urea. CH4 and N2O emissions were measured at the study sites for six years. For the manure plot, a supplement of chemical fertilizer was added to equalize the supply rate of mineral nitrogen (N) relative to that of the fertilizer plots. There were no significant differences in CH4 emissions among the treatment plots, and the effect of fertilizer or manure application was not evident. CH4 emissions tended to be larger at sites with higher soil moisture content. The application of chemical fertilizer or manure increased N2O emissions at all the sites, and there were significant differences among the sites and across different years. Background N2O emissions (N2O emissions at the control plot) had strong positive correlations with air temperature and precipitation, along with weak positive correlations with soil carbon and N content. Therefore, an empirical model (Background N2O emission?=?0.298?x?air temperature?+?0.512?x?soil N content ?3.77) was established. Fertilizer-induced N2O emission factor (EF) had a positive correlation (R2?=?0.50, p?<?0.01) with precipitation (Fertilizer-induced EF?=?0.0022?x?precipitation ?1.3), and increasing precipitation enhanced N2O production through the denitrification process due to applied fertilizer N. There were no significant differences in manure-induced EFs among the sites, and the average was 0.36% except for an outlier.