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In several countries in monsoon Asia, soybean crops are cultivated in upland fields converted from paddies. In such fields, excess soil water often induces extensive damage followed by lower nutrient uptake by this crop. In this study, the effects of flooding during the early growth stage of pot-grown soybeans on arbuscular mycorrhizal (AM) colonization and root nodule formation were investigated. Twenty days after sowing cv. Fukuyutaka, half of the pots were flooded (flooding) and the other half were left unflooded (irrigation). The plants were sampled after 39 days of flooding. Typical morphological alterations to flooding were found, including an enlarged hypocotyl diameter and partial cracking of the surface tissues, and adventitious roots developed on the soil surface. The primary and lateral roots were shorter and the adventitious roots were longer in flooding than in irrigation. In flooding, the ratio of the aerenchyma area to the stele area was 82.5% in adventitious roots. The AM colonization ratio in flooding was significantly lower than in irrigation. The ratio in flooding was markedly low in the primary and lateral roots, but it was not necessarily low in the adventitious roots. Root nodules were formed on the adventitious roots but not on the primary and lateral roots, especially in flooding. These results showing different rates of AM colonization and root nodule formation between the two different types of roots improve the understanding of responses of soybeans grown in paddy-rotated upland fields.