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Ozegahara Mire is the largest alpine mire in Japan. The mire has been preserved as the precious peatland ecosystem with high ecological diversity. After the late 20th century, the mire has been exposed to ecosystem disturbance by mire flooding due to heavy rain as well as invaded Sika deer. Especially, browsing and digging of the mire vegetation by invaded Sika deer have caused considerable impacts on not only vegetation but also physicochemical properties of the mire peat soil. Little information has been published on the effect of flooding and Sika deer disturbance on greenhouse gas emission from the mire. This study aims to provide investigation about the effects of Sika deer disturbance on the soil physicochemical properties and the emission of carbon dioxide (CO2) and methane (CH4) from Ozegahara Mire. Soil and gas samples were collected at 14 fixed plots on 5 sites with and without mire disturbance by Sika deer at eastern Naka-tashiro of Ozegahara Mire through 5 months of 2019 (June to October). Groundwater levels at the study sites were measured each month using hand measurements and continuously using water level loggers. Soil samples were collected with a trowel and gas samples were collected in cylindrical polyvinyl chloride chambers installed on the study sites. Subsequent physicochemical analysis of the soil samples and the gas chromatographic analysis of the gas samples were conducted at the laboratory. Groundwater level displayed similar seasonal change in two sites, being affected by precipitation. The concentrations of NH4+ nitrogen in the disturbed sites were higher than those in the undisturbed sites. Mechanical disturbance of the peat soils by deer resulted in mineralization of organic matter. CO2 and CH4 fluxes from the disturbed sites were lower than those from the undisturbed sites where highest fluxes were recorded in August. Negative correlation was found between CO2 and groundwater level (r = −0.327, p < 0.05), suggesting the importance of groundwater level in greenhouse gas flux. These results indicate the marked influences of the mire disturbance by Sika deer on physicochemical properties of the peat soils and greenhouse gas fluxes at Ozegahara Mire. [ABSTRACT FROM AUTHOR]