Red crown rot is a soybean disease caused by the soilborne fungus Calonectria ilicicola. It gets its name from the small, bright reddish-orange spheres that form on the base of infected stems near the soil line. Once considered a problem limited to the southern United States, red crown rot has been spreading northward through the Midwest since 2018 and is now a growing concern for soybean producers across several states.
What Causes Red Crown Rot
The fungus Calonectria ilicicola lives in the soil and infects soybean roots during the growing season. It was first identified on peanuts in the United States in 1965, then confirmed on soybeans in Japan in 1968 and in North Carolina by 1972. For decades it was mainly a problem in Louisiana and Mississippi, but it appears to have become uncommon in those areas while gaining a foothold farther north.
The pathogen produces both sexual and asexual reproductive structures. In its asexual stage, it was historically classified under the name Cylindrocladium, so older literature may use that name. The fungus survives between seasons in soil and plant debris, and it infects a wide range of legume hosts beyond soybeans, including peanuts, alfalfa, red clover, white clover, crimson clover, vetch, and lupine.
Where Red Crown Rot Is Spreading
Red crown rot was first found in Midwestern soybean fields in Illinois in 2018. Since then it has spread to multiple fields across Illinois and been confirmed in Missouri, Indiana, Ohio, and Michigan. In August 2025, it was detected for the first time in southwestern Minnesota (Rock County), over 400 miles from the nearest known infected location in northwestern Illinois. It has also recently been confirmed in south-central Wisconsin.
This northward expansion is significant because it means growers in major soybean-producing regions who have never encountered the disease now need to know what it looks like and how to respond.
How to Identify Red Crown Rot
Symptoms typically appear during the reproductive growth stages, roughly between early pod development and the beginning of maturity. The earliest sign you’ll notice in the field is yellowing between the leaf veins on upper canopy leaves. This interveinal chlorosis can progress into brown, necrotic patches. In severe cases, plants wilt, defoliate prematurely, and die.
The real diagnostic clues are below the canopy. At and just above the soil line, the base of the stem shows a distinct reddish discoloration. White fungal growth (mycelia) may appear on roots first. Then the hallmark symptom develops: small, bright reddish-orange spheres called perithecia clustered on the stem base and crown. These fruiting bodies are the single most reliable indicator of red crown rot and tend to develop more frequently after periods of high moisture as the plant approaches maturity.
If you split the stem open, you’ll find greyish-brown discoloration of the inner vascular tissue. Below the soil line, roots become deteriorated and rotted in later stages of infection. To scout effectively, you need to dig up plants and inspect the crown and root system rather than just looking at leaves from a standing position.
How It Differs From Sudden Death Syndrome
Red crown rot is easily confused with sudden death syndrome (SDS), because both cause interveinal chlorosis and necrosis on leaves and both can kill plants. The distinction matters because the two diseases are caused by different fungi and may require different management approaches.
The key differences are all found in the lower stem and roots:
- Red crown rot produces reddish discoloration at the stem base, white fungal growth on roots, and distinctive reddish-orange perithecia. When you split the stem, the pith shows greyish-brown discoloration.
- Sudden death syndrome does not produce red discoloration or perithecia at the stem base. When you split the stem, the pith remains white even when roots are severely rotted, though the outer cortex shows brown to gray discoloration.
- Brown stem rot is another look-alike, but it causes discoloration specifically in the pith (the center of the stem) and does not cause rotted roots.
Splitting the stem and examining the pith color is the simplest field-level way to narrow down which disease you’re dealing with. If the pith is white but roots are rotted, it’s likely SDS. If the pith is brown, suspect brown stem rot. If the stem base is red with orange perithecia visible on the outside, red crown rot is your answer.
Managing Red Crown Rot
There is no cure for red crown rot once plants are infected, and management options are currently limited. No soybean varieties in the U.S. have complete resistance, though some show partial tolerance. If you’re in an area where the disease has been confirmed, selecting varieties with the best available partial resistance is a reasonable starting point, even though the differences between varieties are not dramatic.
Crop rotation is the most practical tool. Rotating away from soybeans and all other legume hosts for at least two years can reduce the amount of fungal inoculum in the soil. Non-host crops like corn and small grains are good rotation choices. Keep in mind that rotation reduces the pathogen load but may not eliminate it entirely, since the fungus can persist in soil for extended periods.
Equipment sanitation is an often-overlooked factor. The fungus travels in soil clinging to tillage and harvest equipment, so cleaning machinery between fields helps prevent spreading it from infested areas to clean ones. This is especially important given how rapidly the disease has been moving into new regions.
No fungicide treatments have been widely validated as effective against red crown rot in soybeans. Because the fungus infects through the roots and lives in the soil, foliar fungicide applications don’t reach the site of infection. Research into chemical and biological control options is ongoing, but for now, rotation, variety selection, and preventing soil movement between fields are the primary management strategies available.
Why It’s Becoming More Common
The northward spread of red crown rot likely reflects a combination of factors. Continuous soybean planting builds up soilborne pathogens over time. Movement of infested soil on equipment can introduce the fungus to new fields hundreds of miles from known infections, as the Minnesota detection demonstrated. The pathogen’s perithecia develop most readily under high-moisture conditions near plant maturity, and wet late-season weather in Midwestern states may be creating favorable conditions for the disease to establish and reproduce in regions where it previously couldn’t gain a foothold.
For growers who haven’t seen red crown rot before, the most important step is learning to recognize it. Because it looks so much like SDS from the canopy, it can easily be misidentified or overlooked. Digging up symptomatic plants and checking the stem base for those distinctive red-orange fruiting bodies is the fastest way to tell the difference and get an accurate picture of what’s happening in your field.