Soybean is an important upland crop, but its productivity is often limited by anaerobic stress caused by waterlogging.  The ability to adjust root growth under environmental constraints is an important physiological trait for adapting to an ever-changing environment, and root pruning is an artificial technique for regenerating the root system.  In the present study, we investigated whether root pruning in soybean can effectively alleviate the inhibitory effects of anaerobic stress.  Soybean plants were affected by anaerobic stress at the germination, vegetative stage 1 (V1), and reproductive stage 1 (R1) stages, and then the plants were treated with root pruning just after the stress treatment.  Soybean plants at the germination stage were treated with root cap and tip removals after hypoxia (N2 treatment).  Root cap removal was more effective in suppressing the inhibitory effects of hypoxia than root tip removal (5 mm from the tip).  The shoot dry weights of the soybean plants with and without root cap removal after hypoxia were 51.2 and 73.8% of the control, respectively, while the root dry weights of plants with and without root cap removal after hypoxia were 43.2 and 62.8% of the control, respectively.  As root cap removal effectively enhanced soybean growth after anaerobic stress, the root cap may be the candidate tissue for the stress memory mechanism.  When soybean plants at the V1 stage of growth were affected by anaerobic stress, the branch number, pod weight in the main stem, root length, and root surface area of the soybean plants treated with anaerobic stress at the R1 stage significantly decreased compared with those of the control.  In contrast, root pruning (2 mm from the tip) immediately after the stress treatment enhanced root growth, branch number, and pod weight.  The branch number, pod weight, root length, and root surface area of the plants treated with root pruning were 1.13, 1.14, 1.12, and 1.13 times higher than those of plants treated with anaerobic stress.  Plasmolysis was observed in the root meristem, columella, and cortical cells in soybean roots subjected to anaerobic conditions.  However, damage was not observed in the newly emerged roots after root pruning in plants treated with anaerobic stress.  These results suggested that root pruning is effective in enhancing soybean growth after anaerobic stress.  This effectiveness may be due to the regeneration and elongation of healthy lateral roots during the recovery period.  When soybean plants were affected by anaerobic stress at the R1 stage, root pruning just after the stress treatment was ineffective.  Thus, suppressing the growth reduction due to anaerobic stress at reproductive stages using only root pruning may be difficult.