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The purpose of this study was to investigate muscle activity of the trunk and lower extremities during high vertical stepping in submerged (aquatic) and non-submerged conditions. Twelve participants (mean age 27 years) performed a 40-cm vertical step in water-submerged and non-submerged conditions. Lower limb and trunk muscle activity was recorded using electromyography. A motion capture system was also used to detect angular displacement and forward trunk inclination angle. In submerged conditions, the hip joint demonstrated a larger range of motion, with the electromyogram revealing lower mean values and higher integrated values of muscle activity for some muscles, compared with the non-submerged conditions. It was considered that a low to moderate instantaneous stimulus, but high total stimulus, can be taken on the muscles in the submerged condition compared with the non-submerged condition. Therefore, aquatic rehabilitation training can be effective to maintain or regain stepping ability.