The increase of waterlogged environments is of recent concern due to changes in precipitation regimes and the frequent occurrence of extreme rainfall events. Therefore, it is necessary to comprehend the effects and responses of waterlogging for a better understanding of forests and urban afforestation under changing environments. We investigated root responses of five Japanese afforestation species (Pinus thunbergii, Acer mono, Quercus serrata, Alnus hirsuta and Fraxinus mandshurica) to waterlogging. Potted seedlings grown under natural conditions were waterlogged at soil-surface level for 2.5 months during the growing season. The in-growth core method was used to distinctively measure root growth. As a result, fine root growth during the waterlogging period was significantly decreased for P. thunbergii, A. mono and Q. serrata. Furthermore, root tissue density (RTD) of pre-existing roots was decreased, which suggests root damage such as partial root death and root decay. On the other hand, for A. hirsuta and F. mandshurica, fine root growth was not decreased under waterlogging. For A. hirsuta, although fine root growth continued at the top half, it was decreased at the bottom half. Root damage such as a decrease in RTD was observed for pre-existing roots. For F. mandshurica, root growth continued at the top and bottom half, and root damage of pre-existing roots was not observed at either the top or the bottom. From our results, it was suggested that P. thunbergii was most sensitive, followed by A. mono and Q. serrata. A. hirsuta and F. mandshurica were relatively tolerant; however, the most tolerant was F. mandshurica, as pre-existing roots were not damaged by waterlogging. Overall, root responses could be grouped into three groups: (1) P. thunbergii, A. mono, Q. serrata; (2) A. hirsuta; (3) F. mandshurica. The observed responses may reflect the species’ natural distributions.