Pythium Pretenders: Differentiating Between Common Seedling Diseases

Pythium is a pathogen that lives in soil and often wreaks havoc on row-crop operations. The disease causes about $25 million in annual damage to the North American corn crop.¹ Pythium and other seedling diseases also destroyed nearly 23.7 million bushels of soybeans across 29 U.S. states in 2024.²

To make matters worse, Pythium is often tough to diagnose because it presents symptoms similar to those of other seedling diseases, insects and nematodes. Learning to correctly diagnose Pythium and to spot the pretenders (Phytophthora, Fusarium, Rhizoctonia, nematodes and insects) can mean the difference between properly managing crops throughout the growing season — or committing critical errors that can prove costly.

Pythium in corn and soybeans: top symptoms and scouting tips

Cold soil temperatures below 60 F and wet fields, especially low-lying or compacted areas, create a prime breeding ground for Pythium.³ Pythium symptoms are found in seedlings, so it’s a good idea to begin scouting soon after planting, especially if planting has occurred earlier than usual. In soybeans, this means studying plants from VE through V2 stages for signs of disease. In corn, examine plants at VE stage, then again in two weeks and, finally, after another two-week interval.⁴

Common Pythium symptoms include:

• “Rat-tailing”: The outer cortex of plant roots is very wet, and it falls off when rubbed between the fingers, leaving only inner tissues behind.⁵
• Color irregularities: Roots appear unhealthy, with color somewhere between yellow and brown.
• Rotted mesocotyl: The seed “packaging” that eventually produces leaves withers instead of appearing as a nice, healthy white.

With those key signals in mind, it’s time to turn your attention to a lineup of bad guys trying to pass themselves off as Pythium.

Pythium pretenders: the frustrating four

Although several seedling diseases, insects and nematodes can produce Pythium-like symptoms, four are particularly aggravating. Here’s how you can distinguish Pythium in corn and soybeans from these pretenders.

(Jennifer Rojas et al.)

Pythium symptoms versus Phytophthora root and stem rot of soybeans and corn

As with Pythium, Phytophthora root and stem rot causes symptoms such as seedling decay. Seedlings can rot even before a plant has emerged from the soil, effectively crumpling shortly after breaking through the soil.

When trying to differentiate between Pythium and Phytophthora, you can compare the following symptoms:

• Stem color: When scouting, cut a few stems at the plant base near the soil. A dark center in the stem likely reveals Phytophthora, not Pythium.
• Late-stage damage: If plants seem to be struggling past V5, you might be dealing with Phytopthora. Pythium generally kills plants only at V5 or earlier.⁶

Pythium symptoms versus Fusarium in corn and soybeans

To differentiate between Pythium and Fusarium, compare the following conditions and symptoms:

• Drier soils: Diseased plants growing in drier conditions, sandy soil or even nicely drained loam-type soil can harbor Fusarium, rather than Pythium.
• Root color: Both corn and soybeans exhibit signs of Fusarium in a way that’s distinct from Pythium. In corn, Fusarium often causes root systems to be smaller with brown or black coloring. In soybeans, similar color issues emerge, typically on the lower part of plant roots.

Pythium symptoms versus Rhizoctonia in corn and soybeans

Distinct disease markings are a key indicator that Rhizoctonia, not Pythium, is at work. You should scout for these conditions and symptoms:

• Well-drained conditions: Rhizoctonia typically occurs in drier areas with sandy and loamy soils, whereas Pythium thrives in wet, water-logged soils.
• Lesions and other tissue problems: Rhizoctonia manifests as reddish-brown leisons on corn and soybean stems that appear just above the soil. In corn, also look for seedlings that die before emergence and for mesocotyl tissue that’s dark and can be easily rubbed off, leaving white vascular tissue intact.

Pythium symptoms versus nematodes and insect damage

Damage from nematodes and insects can also be hard to distinguish from Pythium. But there are some telltale signs. Among them:

• Sickly plants: Look for yellowing or stunted corn and soybeans, which can signal potential insect damage. (Nematodes, often called “silent killers,” don’t leave this kind of symptom.)
• Knotty roots: Nematodes can leave cysts or knots on roots, whereas Pythium does not.⁷

Scout with care for Pythium symptoms in corn and soybeans

By knowing the symptoms of Pythium and those of other pests and diseases that present similarly, you can work with your trusted adviser to develop a management plan for corn and soybeans. For both corn and soybeans, consult with your seed supplier for the appropriate hybrid and variety to protect from Pythium, as well as seed treatment packages available with the seed. For soybeans, an additional seed treatment of Obvius® Plus offers another layer of protection from pythium and other seedling diseases.

Experts are available to help you make your decisions. Reach out to your seed retailer, a nearby extension office agent, or a seed company professional like your regional BASF representative.

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Endnotes

1. Rojas, Jennifer A., et al. “Managing Seedling Diseases of Corn Caused by Pythium spp.” Plant Health Progress, vol. 22, no. 3, 2021, pp. 163–173. The American Phytopathological Society, https://doi.org/10.1094/PHP-02-21-0046-FI.
2. Mueller, Daren S., et al. Soybean Disease Loss Estimates from the United States and Ontario, Canada—2024. Crop Protection Network, 2024, https://cropprotectionnetwork.org/publications/soybean-disease-loss-estimates-from-the-united-states-and-ontario-canada-2024.
3. Sweets, Laura E., Doug Jardine, and Travis W. Procter. Seedling Diseases of Soybean. Kansas State University Agricultural Experiment Station and Cooperative Extension Service, Aug. 2020, https://soybeanresearchinfo.com/wp-content/uploads/2020/08/MF3134-1.pdf.
4. Bessin, Ric. Insect Pest Management in Corn. University of Kentucky Cooperative Extension Service, 2019, https://ipm.ca.uky.edu/files/ipm2corn2.pdf.
5. Dami, Ijaola. “Pythium- an early season pain in corn and soybeans.” Illinois Field Crop Disease Hub, University of Illinois Extension, 11 Apr. 2023, http://cropdisease.cropsciences.illinois.edu/?p=1071.
6. Mueller, Dylan. “Conditions Favor Seedling Diseases in Early-Planted Corn and Soybeans.” CropWatch, University of Nebraska–Lincoln, 5 May 2022, https://cropwatch.unl.edu/2022/conditions-favor-seedling-diseases-early-planted-corn-and-soybeans/.
7. Creswell, Tom, and Jamal Faghihi. “Soybean Nematodes.” Purdue University Department of Entomology, https://ag.purdue.edu/department/entm/extension/nematology/soybean-nematodes.html. Accessed 1 Apr. 2025.