The antifungal efficacy of smoke-water on damping-off caused by Pythium sp. was evaluated both in vitro and in vivo. Smoke-water was generated by burning plant material and bubbling the smoke through water; its effect on the morphology of Pythium sp. was investigated by scanning electron microscope (SEM). Mycelia growth and oospore production of the fungus were significantly inhibited when cultured on water agar amended with smoke-water at 0%, 0.5%, 1%, 1.5%, 2%, 2.5%, 3%, 3.5%, 4%, 4.5%, or 5%. In growth chamber experiments with potted seedlings growing in peatmoss, papaya plants treated with smoke-water exhibited reduced symptoms of damping-off when compared with control plants treated with water. Furthermore, the pots treated with 1.5% or higher smoke-water did not show any symptoms of damping-off disease. Plant height significantly increased with treatment by higher concentrations of smoke-water. Maximum plant height was observed with treatment of 1% smoke-water or higher concentrations. One day after smoke-water application, SEM observations of the Pythium sp. revealed loss of structural integrity, abnormal degradation, deformation, abnormal lysis, cytoplasmic leakage, and hyphal slimming. This study showed that the addition of smoke-water to soil exerted significant disease suppression against Pythium sp., leading to improved growth of papaya seedlings.