Flooding and drought are the two different forms of water stress that adversely affect the growth and development of soybean plant in particular at early stage. Ascorbate peroxidase (APX) is a known antioxidant enzyme that plays key role in abiotic stresses. To investigate the changes in APX in soybean under drought and flooding stresses, western blotting, enzyme activity assay and biophoton emission techniques were used. Flooding stress was imposed by adding excess amount of water in the sand and drought by withholding water supply. Under flooding stress, a decrease in APX was detected with time. Completely opposite trend was evident in hypocotyl and root of plants exposed to drought. Western blotting and APX activity results are complementary to each other. Biophoton emissions further confirmed the increasing and decreasing trend of APX under drought and flooding stress, respectively.