In Japan, soybean is usually cultivated in fields that have been converted from rice paddies, and poor seedling establishment due to pre-emergence seedling damping-off is often observed during the rainy season. In this study, the factors that cause the damping-off in flooded soil were investigated under high soil moisture conditions in a greenhouse and in agricultural fields. In sterilized soil sampled from a soybean field, seedlings emerged well under 48-hr flooded conditions. In unsterilized soil, soybean seeds treated with the fungicide, mancozeb +metalaxyl exhibited much higher emergence rates even under 48-hr flooded conditions than the seeds treated with oxytetracycline +streptomycin, benomyl, or flutolanil. Pythium, Phytophthora, Mucorales, Trichoderma, Geotrichum-like microorganisms, and some fungi producing conidia in a false head, were isolated from decayed seedlings. Of the isolated microorganisms, oomycete microorganisms, Pythium helicoides, other Pythium sp., and Phytophthora sp. were pathogenic to soybeans under flooded conditions. As the length of the flooding period increased, pre-emergence seedling rot also increased. However, the pathogenic oomycetes rarely caused pre-emergence seedling rot under conditions without flooding. Furthermore, under flooded conditions, the damage caused by these pathogens was reduced by treating the seeds with mancozeb+metalaxyl. These results indicate that oomycete microorganisms are involved in pre-emergence seedling damping-off under flooded soil conditions.