The increase of waterlogged environments is of recent concern due to changes in precipitation regimes and increase of extreme water events. Therefore, it is critical to comprehend responses and sensitivity of tree species to waterlogging stress for better understanding forests and urban greenery under changing water conditions. In our study, a potted seedling experiemnt was conducted on Pinus thunbergii, which is often planted along costal areas. A 2-month waterlogging treatment was condcuted during the growing season. For the waterlogging treatment, two different water tables were set; one to soil surface (full waterlogging) and the other at half height of the pot (half waterlogging). All seedlings were grown at a experimental nursery from April 2019 to October 2019 under natutal conditions. Investigations were made on root growth and, changes in morohology and spatial distribution, in relation with above-ground responses, being transpiration. As a result, transpiration was decreased under waterlogging and was more decreased at the full waterlogging treatment. However, transpiration increased under half waterlogging at the latter period of the waterlogging treatment, suggesting acclimation by change in root spatial distribution, where fine root growth was increased at the upper half of the soil layer during the waterlogging treatment.