Soybean Seed and Seedling Diseases

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Disease Facts

  • Pathogens that attack soybean seeds and seedlings (Phytophthora, Pythium, Rhizoctonia and Fusarium) survive in diseased plant material and in the soil.
  • These diseases are most common when soil is very wet in the first few weeks after planting, especially in heavy, poorly drained, compacted or high-residue fields.
  • Diagnosing soybean seedling diseases can help in understanding later symptoms and final yields, and managing these diseases in future years.
  • Pythium and Fusarium are more likely to occur when soil temperatures are cooler (<60 F). Phytophthora and Rhizoctonia are more likely to be the culprit if soils are warmer (70 to 80 F).
  • Commercial soybean varieties vary little for resistance to seedling pathogens (except for Phytophthora). Pioneer Hi-Bred does not rate varieties for resistance to these other diseases.
  • Management of seed and seedling disease is best achieved through sound planting practices to minimize stress, and through use of fungicide seed treatments.
  • Pioneer Premium Seed Treatment helps protect against all of these stand-reducing pathogenic fungi.

Table 1. Summary of seed and seedling disease symptoms*.

Growth Stage
Seed rot /
Soft decay of seed; missing seedlings in row.
Seedling mortality (damping off, seedling blight ) /
Wilting, yellow leaves. Necrotic lesions on stems. Death of seedlings can occur quickly. Leaves remain attached to stem.
Root and lower stem decay /
Reddish-brown lesions on taproot and hypocotyl; often superficial. Phytophthora causes brown lesions on stem above soil line.


  • Prefers cold soil temperatures (<60 F); may be the first soybean disease found in a growing season.
  • High-residue fields and heavy or compacted soils are at higher risk because of cooler, wetter conditions.
  • Pathogen may attack seeds before or after germination; seeds killed before germination are soft and rotted with soil adhering to them.
  • Plants may be killed by "damping off" before or after emergence. On infected plants, the hypocotyl becomes narrow and is commonly "pinched off" by the disease.

Photo: Symptoms of Pythium infection
Photos above and below: symptoms of "damping off" of just-emerged soybean
seedlings due to Pythium infection.
Photo: soybean seedling emergence - Symptoms of Pythium infection

  • Emerged plants may be killed before the first true leaf stage. These plants have a rotted appearance.
  • Diseased plants may easily be pulled from the soil because of rotted roots.


  • Is more common in wet soils or moderately wet soils where germination is slow or emergence is delayed.
  • Infection is characterized by a shrunken, reddish-brown lesion on the hypocotyl at or near the soil line.
  • Infection may be superficial, causing no noticeable damage, or may girdle the stem and kill or stunt plants.

Photo: Reddish-brown lesion on soybean hypocotyl near the soil line.
Photo: Reddish-brown lesion on soybean hypocotyl near the soil line is a characteristic
of Rhizoctonia infection.

  • Normally appears as the weather becomes warm (~80 F); more often seen in late-planted soybean fields.
  • Causes loss of seedlings (damping off) in small patches or within rows; is usually restricted to the seedling stage.

Photo: Stand loss due to Rhizoctonia infection. Microenvironments favorable for disease development may lead to losses in 'patches', or in sections of rows.
Stand loss due to Rhizoctonia infection. Microenvironments favorable for
disease development may lead to losses in "patches" or in sections of rows.


  • Infection is caused by a complex of different species that prefer different conditions; some prefer warm and dry soils, while others prefer cool and wet soils.
  • Some species attack corn, wheat and other host plants.
  • Causes light to dark brown lesions on soybean roots that may spread over much of the root system.
  • May attack the taproot and promote adventitious root growth near the soil surface, and may also degrade lateral roots, but usually does not cause seed rot.

Photo: Dead plant due to Fusarium infection.
Dead plant due to Fusarium infection, with healthy plants in background.
Less severe infections may degrade roots without resulting in plant death.

Photo: Stand loss due to Fusarium infection.
Stand loss due to Fusarium infection. Note the "patchy" nature of infection
occurring in a specific area of the field.


*Table 1 adapted from: University of Wisconsin Field Crops Plant Pathology - Plant Health Initiative

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