An Overview of Soybean Seedling Diseases

Updated in 2026, this version replaces the 2020 An Overview of Soybean Seedling Diseases publication.

Soybean seedling diseases are often the cause of reduced plant stand and can lead to significant economic losses each year. Diseased seedlings are often less vigorous, and severe stand loss may require replanting of affected areas. Seedling diseases are most prevalent when wet weather follows planting and are more common in compacted or poorly drained soils, or where seedlings have been injured by herbicides (Figure 1). As soybean planting dates continue to shift earlier, the risk of seedling disease development increases.

Diagnosing seedling diseases in the field can be difficult since the symptoms of various seedling blights are similar, and affected seedlings often decompose quickly. This publication discusses the characteristics of the major pathogen groups that cause seedling diseases, describes injury symptoms that may resemble these diseases, and briefly addresses how to manage these seedling diseases.

The soybean seedling diseases that are most commonly observed on soybean are:

1. Fusarium root rot

2. Rhizoctonia seedling blight

3. Phytophthora root rot

4. Pythium seedling blight

Fusarium Root Rot (Fusarium spp.)

Many species of Fusarium are common in soil and can infect soybean seedlings. Infected plants may be stunted and spindly, with brown to black lesions on the roots (Figure 2) and poorly developed root systems.

 In severe cases, seedlings may die before emerging. Species of Fusarium can infect plants under a wide variety of environmental conditions. Fusarium root rot is often associated with plants that are already stressed.

Rhizoctonia Seedling Blight (Rhizoctonia solani)

Rhizoctonia seedling blight is caused by the fungus Rhizoctonia solani. Its most characteristic symptom is a reddish-brown lesion on the lower stem or hypocotyl, usually at the soil level (Figure 3). Lesions on the diseased stem appear sunken (canker-like) and dry, and can girdle the hypocotyl.

 This disease can occur across a wide range of soil conditions. Affected plants typically appear in patches or in rows in a field. Although temperature and moisture requirements for infection and disease progression vary, this disease is most common in warm and moist (but not saturated) soils. Stressed seedlings may be more vulnerable.

Phytophthora Root and Stem Rot (Phytophthora spp.)

Phytophthora root rot of soybean is caused by the oomycetes Phytophthora sojae and P. sansomeana. Infected plants occur alone or in patches within a field (Figure 4).

The stems of Phytophthora-infected seedlings are typically mushy and water-soaked. Overall, infected seedlings will be wilted and stunted. These symptoms resemble those of many other seedling disease pathogens. Phytophthora sojae can also cause a stem rot of mature plants, characterized by chocolate-brown stem lesions that extend from the soil line. Phytophthora root rot occurs across many environments but is most common in warm (>60°F/15°C) and wet soils.

Pythium Seedling Blight (Globisporangium spp. - formerly Phythium spp.)

Globisporangium (formerly Pythium), a group of oomycetes, includes multiple species that can cause soybean seedling blight and seed rot. These soilborne pathogens cause symptoms similar to those caused by species of Phytophthora. Typical symptoms include rotten, mushy seed or seedlings with poorly developed roots. Water-soaked lesions may be present on the hypocotyl or cotyledons (Figure 5).

Pythium seedling blight can develop across a range of temperatures, but high soil moisture increases the likelihood and severity of the disease. Consequently, symptoms are most severe in poorly drained soils and areas prone to flooding. Recent research indicates that many species of Globisporangium common in the northern United States and Canada infect plants at lower temperatures (50-77°F/10-25°C), whereas species more prevalent in the southern United States tend to infect at warmer temperatures (85-95°F/30-35°C).

Diagnosing Seedling Blights

Seedling diseases are difficult to correctly diagnose in the field and are easily mistaken for other problems (such as herbicide injury or environmental damage). In addition, seedlings may be affected by more than one seedling disease in a field at the same time.

For these reasons, we recommend sending injured soybean seedlings to a local diagnostic lab to confirm the cause before implementing a disease management program. Obtaining an accurate diagnosis is the first step in determining a management strategy. In addition, it may also be necessary to identify the pathogen species(i.e., Phytophthora sojae vs. Phytophthora sansomeana) to customize management, as fungicide efficacy and varietal resistance may vary depending on pathogen species.

A few examples of disorders that can cause similar symptoms to soybean seedling blights are listed below:

Conditions With Similar Symptoms

Fluopyram Fungicide Effects

The fungicide fluopyram (ILEVO, BASF) is marketed as a seed treatment for the management of sudden death syndrome (SDS) and soybean cyst nematode (SCN). In field situations where fluopyram has been applied as a seed treatment, soybean cotyledons may appear discolored, resembling disease or herbicide injury. The discoloration occurs because the fungicide is moderately systemic within the soybean plant, so it will naturally move to the plant’s “sinks,” the roots and cotyledons. 

This accumulation can result in phytotoxicity, causing the tips of the cotyledons to turn yellow-brown. This necrosis is typically uniform on seedlings grown from ILEVO-treated seed; however, cool, wet conditions can exacerbate these symptoms. Research conducted by several land-grant universities and the Ontario Ministry of Agriculture, Food and Agribusiness (OMAFA) demonstrated that this phytotoxicity (also referred to as “halo effect”) does not result in long-term stunting or yield losses.

How to distinguish fluopyram effects from seedling diseases: Symptoms of fluopyram phytotoxicity will be consistent across seedlings treated with the fungicide and present on edges of cotyledons, but not on roots or stems.

Preemergence Herbicide Damage

Preemergence herbicides can also damage soybean seedlings, particularly when cool temperatures coincide with rain shortly after seedlings begin to emerge from the soil. Preemergence herbicides, typically PPO-inhibitors or photosynthetic inhibitors (e.g., flumioxazin, fomesafen, metribuzin, saflufenacil, sulfentrazone), can injure plants growing in cold, wet soils. Soybean is typically able to metabolize these herbicides, but when plant metabolism slows due to stress (such as cold temperatures), herbicide injury can occur (Figure 7).

Preemergence herbicide injury also occurs when heavy rains splash concentrated droplets of residual herbicide from the soil onto emerged seedlings (Figure 8). Spotty necrosis can occur on any exposed portion of the plant where splashing occurred. These herbicides can cause symptoms similar to the phytotoxicity caused by ILEVO^®.

Preemergence herbicide injury is more likely to occur in sandy soils with low organic matter (OM) than in loam or clay soils with higher OM. Also, some soybean varieties are more sensitive to these herbicides than others. Herbicide sensitivity information is available from some, but not all, seed companies.

How to distinguish preemergence herbicide damage from seedling diseases:Check spray application records to determine if a preemergence herbicide application occurred on the field in question. Symptoms of preemergence herbicide damage are typically consistent on all treated plants, whereas seedling blights are observed in patches.

Environmental and Planting Issues

Frost or freeze damage is evident several days after the event, and results in a brown-purple, water-soaked appearance on the hypocotyl and cotyledon (Figure 9). Soil crusting may prevent or delay seedling emergence, causing the seedling to die before it can emerge. 

Several factors can worsen environmental issues, including uneven planting depth, inconsistent seed spacing, and incomplete closure of the seed furrow. These factors can create gaps in the row, where seedlings may be missing or only partially emerged.

How to distinguish environmental or planting issues from seedling diseases: Seedlings may exhibit above-ground injury from a frost, but roots should appear healthy. Planting issues will result in gaps or patchy emergence, but the seedlings present will appear healthy (Figure 10). Seedlings that are crusted over and die prematurely may be difficult to distinguish in the field from those that die due to seedling blights and therefore require laboratory diagnosis.

General Management

The organisms that cause seedling diseases can survive in soil for many years, and most are capable of infecting other crops such as alfalfa, corn, sugar beet, and wheat, and various weed species. As a result, crop rotation alone may not be sufficient to manage these diseases. Short rotations between soybean crops can allow seedling disease organisms to build to high levels in the soil.

Seedling diseases are more prevalent in no-till or reduced tillage systems, where soils typically warm more slowly in the spring and retain more moisture. In these systems, additional management practices, such as fungicide seed treatment, may be needed to manage seedling blights. 

Fungicide seed treatments vary in efficacy, and products that control diseases caused by Globisporangium, Phytophthora, and Pythium (such as ethaboxam, metalaxyl (-M), mefenoxam, and oxathiapiprolin) generally do not control the species of Fusarium and Rhizoctonia. Conversely, fungicides active against Fusarium and Rhizoctonia have little effect on oomycetes.

Efficacy can also depend on the pathogen strain, as some strains may be less sensitive to certain fungicides. Accurate diagnosis of seedling blights present in a particular field, if possible, down to the species level, helps ensure the most effective seed treatment is selected. 

Fungicide seed treatment efficacy guides are updated annually and available through the NCERA-137 Soybean Disease Working Group. For a current list, see Fungicide Efficacy for Control of Soybean Seedling Diseases (CPN-1020).

Acknowledgements

Authors

Kiersten Wise, University of Kentucky; Horacio Lopez-Nicora, The Ohio State University; Carl Bradley, University of Kentucky; Dylan Mangel, University of Nebraska Lincoln; Bill Johnson, Purdue University; Travis Legleiter, University of Kentucky; Mark Licht, Iowa State University; Daren Mueller, Iowa State University; Martin Chilvers, Michigan State Unviersity; Adam Sisson, Iowa State University; Albert Tenuta, Ontario Ministry of Agriculture, Food, and Agribusiness; Heather Young-Kelly; University of Tennessee.

Reviewers

Tom Allen, Mississippi State University; Mandy Bish, University of Missouri; Maira Duffeck, Oklahoma State University; Travis Faske, University of Arkansas; Dean Malvick, University of Minnesota; Trey Price, LSU AgCenter; Damon L. Smith, University of Wisconsin-Madison; Darcy Telenko, Purdue University.

Sponsors

The authors thank The United Soybean Board, North Central Soybean Research Program, Grain Farmers of Ontario, North Central Integrated Pest Management Center, and United States Department of Agriculture - National Institute of Food and Agriculture for their support.

How to cite: Wise, K., Lopez-Nicora, H., Bradley, C., Mangel, D., Johnson, B., Legleiter, T., Licht, M., Mueller, D., Chilvers, M., Sisson, A., Tenuta, A., Young-Kelly, H. 2026. An Overview of Soybean Seedling Diseases. Crop Protection Network. CPN-1008. doi.org/10.31274/cpn-20190620-023.