An Overview of Charcoal Rot of Soybean

Updated in 2026, this version replaces the 2016 An Overview of Charcoal Rot of Soybean publication.

Charcoal rot of soybean (Figure 1) is caused by the soilborne fungus Macrophomina phaseolina (Figure 2), which can infect around 100 agricultural crop and weed species. This disease had historically been primarily a southern soybean problem, but is now established as an important issue across the U.S. and Ontario, Canada. Recent weather trends — warmer summer and winter temperatures and reduced rainfall — have increased the frequency of conditions favorable for disease development. Yield losses from charcoal rot are highly variable, but farmers can reduce crop injury by implementing best management practices based on a better understanding of this disease.

Disease Development

The charcoal rot fungus survives in soil and plant residue as small, hard black structures known as microsclerotia (Figure 3). Many agronomic plants serve as hosts to this causal organism, which means that pathogen inoculum can be present in residues of several important rotation crops, including corn, soybean, grain sorghum, sunflowers, and many weed species.

Infected soybean seed can also serve as a source of inoculum, although seed infection may not always be apparent with microsclerotia embedded in cracks in the seed coat or on the seed surface. When soybean roots come into contact with or grow close to microsclerotia, the latter germinate and infect the roots (Figure 4). This can occur throughout the season, affecting even young seedlings when soils are wet. Once the roots are infected, the fungus will slowly colonize both root and stem tissue until soybean plants reach the reproductive growth stages, from flowering (R1) to full maturity (R8).

After pod fill is complete, colonization rapidly increases as the plant fully matures. The fungus grows within the roots and stem and interferes with water uptake by clogging vascular tissue with fungal growth and newly formed microsclerotia (Figure 5).

Many environmental factors affect microsclerotia survival, root infection, and disease development. For example, microsclerotia can remain viable for many years in dry soils, but cannot survive for more than a few weeks in saturated soils. Soil pH may not directly affect microsclerotia survival, but can influence the abundance of microsclerotia (inoculum density). For example, in South America, it has been reported that the highest levels of the charcoal rot pathogen are found in acidic soils with high clay content.

Although infection by the charcoal rot fungus can occur early in the season, with colonization progressing throughout the season, symptoms may not develop unless the infected plants are stressed. These conditions typically involve extreme heat and drought, and the timing and duration of these conditions will influence the type and severity of symptoms that develop.

Charcoal rot symptoms are most prevalent during hot and dry weather conditions, especially during the soybean reproductive growth stages. However, disease and subsequent yield losses have been observed in irrigated systems and in crops with no visible symptoms.

Symptoms/Signs of Charcoal Rot

The characteristic sign of charcoal rot is the presence of microsclerotia in root and stem tissue, which may not be visible until plant maturity or death.

In soybean, the charcoal rot fungus can infect seed, seedlings, or mature plants. If infected at the seed or seedling stages, plants may not emerge or seedlings may become discolored and die. Plants infected early in the season may not show symptoms until midseason or later. In more mature plants, the fungus can cause reduced vigor, yellowing, and wilting. Patches of these symptoms in a field are usually the first indication of a problem.

Premature death with leaves still attached to the plant is the most common symptom. Within a field, symptoms develop first in the driest parts of the field. Common areas affected include hillsides, sandy areas, terrace tops, compacted headlands, or along the edges of fields where trees may compete for moisture.

Plants affected by charcoal rot may initially have a gray discoloration on the lower woody portion of the stem (Figure 6). Microsclerotia will be visible on the lower portion of the plant, often just under the outermost layer of stem tissue (Figure 7). Microsclerotia are less than 1/25 of an inch (1 mm) in size. To the naked eye, it will look as if the root or stem has been “peppered” with black spots. Upon closer inspection with a hand lens, individual microsclerotia can be seen within the plant tissue. In some instances, a fine line of stem decay and discoloration can be observed in cross-sections of soybean plants (Figure 8).

Charcoal rot is hard to diagnose in dry years, as it is difficult to distinguish its symptoms from those of general drought stress. However, plants with charcoal rot die more quickly during periods of drought stress than those without the disease. To accurately identify charcoal rot, dig symptomatic plants and split the lower stems and taproot to confirm discoloration as light gray or silver (Figure 6), and the presence of black streaks (Figure 8) and microsclerotia (Figure 7).

Diseases With Similar Symptoms

Charcoal rot-affected plants have microsclerotia in the lower stem and roots, which can help differentiate it from other diseases. However, some charcoal rot symptoms can be mistaken for those of other diseases.

Pod and Stem Blight (Diaporthe/Phomopsis spp.)

Pod and stem blight can occur during warm, humid weather, especially when soybean plants are maturing. Infection results in the production of small, black specks, called pycnidia, which can be confused with microsclerotia. Pycnidia can form on stems, petioles, pods, and seeds.

How to distinguish pod and stem blight from charcoal rot: Pycnidia are generally larger than microsclerotia and are present in linear rows on the outside of stems, whereas microsclerotia of the charcoal rot fungus form throughout (inside) the taproot and lower stem; leaves do not remain attached as they do when charcoal rot affects soybean.

Phytophthora Root and Stem Rot (PRR — Phytophthora sojae)

Phytophthora root and stem rot (PRR) occurs in wet, waterlogged, compacted soils. Symptoms of this disease generally appear during or shortly after the occurrence of waterlogged soil conditions.

How to distinguish PRR from charcoal rot: Stems of Phytophthora-infected plants have characteristic dark brown lesions visible on the outer stem tissue that are continuous from the roots and up the lower stem.

Saprophytic Fungi

Once soybean plants have senesced, many fungal organisms will use dead plant tissue as a food source. These fungi, called saprophytes, do not infect the plant during the season but survive by colonizing dead tissue. Black fungal structures produced by these organisms may be mistaken for charcoal rot microsclerotia.

How to distinguish saprophytic fungi from charcoal rot: Soybean that senesce early or prematurely will be more heavily colonized by saprophytic fungi, giving stems a dark appearance. In these situations, be sure to examine the inner plant tissue of the stem and root to determine if microsclerotia are present.

White Mold (Sclerotinia stem rot — Sclerotinia sclerotiorum)

White mold (Sclerotinia stem rot) is typically more of a problem in years with rainy and cool environmental conditions that occur at flowering (R1). Lesions develop on the nodes and expand up the stems.

How to distinguish white mold from charcoal rot: Sclerotinia-infected plants can be identified by the presence of a fluffy white growth on the outside of stems. In addition, the sclerotia produced by the sclerotinia stem rot fungus, which are also hard and black, are much larger than charcoal rot microsclerotia.

Soybean Cyst Nematode (SCN — Heterodera glycines)

Subtle symptoms of soybean cyst nematode (SCN) infection include uneven plant height, a delay in canopy closure, or early maturity. Severely infected plants may be stunted with yellow foliage.

How to distinguish SCN from charcoal rot: White SCN females are most readily observed on soybean roots starting about six weeks after crop emergence.

Stem Canker (Diaporthe spp.)

How to distinguish stem canker from charcoal rot: Stem canker is distinguished by the production of brown to black, slightly sunken lesions or “cankers” that start at the nodes and grow completely around the stem. These will typically not be at the soil line, extending upward like Phytophthora root and stem rot.

Sudden Death Syndrome (SDS — Fusarium virguliforme)

Symptoms of sudden death syndrome (SDS) are expressed as yellowing and necrosis between the veins of leaflets. Veins of symptomatic leaves will remain green. Leaflets will eventually curl or shrivel and drop off, leaving only the petiole.

How to distinguish SDS from charcoal rot: Symptoms of SDS occur between the veins rather than causing generally brown, crinkled leaves.

Red Crown Rot (RCR - Calonectria ilicicola)

Symptoms of red crown rot (RCR) begin with yellow blotches on the leaves that progress to yellowing and death between the veins and leaflets. Leaves will die prematurely. Red coloration will typically form near the soil line.

How to distinguish RCR from charcoal rot: After periods of moisture late in the growing season, discolored stem areas become flush with white hyphae and red/rusty brown spore-bearing structures. Roots are rotted and plants are easily removed from the soil.

Management

Management of charcoal rot includes the use of resistant varieties when available and certain cultural practices, including those that conserve soil moisture. No fungicide seed treatments have been identified that offer consistent control of charcoal rot.

Resistant Varieties

Efforts to identify resistance to charcoal rot have focused largely on soybean varieties adapted to the southern U.S. (maturity group IV and later). Although partial resistance has been identified, the level of resistance is moderate at best and must be combined with additional  management strategies. To date, our knowledge of resistance to charcoal rot in northern varieties (maturity groups 0–III) is limited. Researchers are currently evaluating commercial varieties and breeding lines for partial resistance to charcoal rot. Because resistance levels vary by region, contact your seed supplier to identify specific varieties that meet your farm’s performance and soil requirements.

Tillage

Soybean direct-seeded in no-till systems typically have reduced levels of charcoal rot compared to soybean under conventional tillage. This is because no-till systems often result in greater  soil microbial activity, in some cases greater available soil nutrients, and generally healthier plants. In addition, no-till systems can aid in soil moisture conservation, which may also reduce the severity of charcoal rot.

Irrigation Management

Colonization of roots by M. phaseolina can be reduced in irrigated soybean compared to nonirrigated soybean. However, root colonization still occurs in irrigated production systems. Although supplemental irrigation can reduce the damage caused by charcoal rot when soil moisture is low (e.g., under drought conditions), colonization by M. phaseolina can result in the production of microsclerotia, which will increase the level of inoculum for subsequent host crops.

Rotation

Rotation to nonhost crops such as wheat for one or two years should be considered part of a charcoal rot management plan in problematic fields. Although corn, sunflowers, and other crops are hosts, research has shown that there are strains of the fungus that have host preferences. For instance, some strains prefer soybean while others prefer corn or sunflower. Therefore, rotation with any other crop can be beneficial and the longer the rotation, the better.

Seeding Rate

Reduced seeding rates will not prevent root colonization by the charcoal rot fungus. However, using reduced seeding rates can decrease crop stress, which in turn helps minimize yield losses from charcoal rot.

Best Management Practices

Management of charcoal rot of soybean can include one or all of the following strategies:

• Use varieties with the highest level of resistance available in a maturity group appropriate for your region.

• Use no-till systems to increase soil microbial activity and conserve soil moisture, which can reduce charcoal rot.

• Use supplemental irrigation to slow colonization of the plant by the charcoal rot pathogen and reduce symptom severity during drought conditions.

• Rotate to nonhost crops (such as wheat) for one to two years in fields with a history of charcoal rot.

• Avoid excessive seeding rates to reduce crop stress and minimize loss to charcoal.

Acknowledgements

Authors

Damon Smith, University of Wisconsin-Madison; Marty Chilvers, Michigan State University; LeAnn Lux, North Carolina State University; Daren Mueller, Iowa State University; Madalyn Shires, South Dakota State University; Richard Wade Webster, North Dakota State University; and Kiersten Wise, University of Kentucky.

Reviewers

Tom Allen, Mississippi State University; Alyssa Betts, University of Delaware; Mandy Bish, University of Missouri; Maira Duffeck, Oklahoma State University; Travis Faske, University of Arkansas; Horacio Lopez-Nicora, The Ohio State University; Dean Malvick, University of Minnesota; Trey Price, LSU AgCenter; Darcy Telenko, Purdue University; Albert Tenuta, Ontario Ministry of Agriculture, Food and Agribusiness.

Sponsors

The Soybean Disease Management series is a multi-state collaboration sponsored by the North Central Soybean Research Program (NCSRP) through the Soy Checkoff. This project was funded in part through Growing Forward 2 (GF2), a federal-provincial territorial initiative. The authors thank the United States Department of Agriculture - National Institute of Food and Agriculture, the Grain Farmers of Ontario, and United Soybean Board for their support.

How to cite: Smith, D., Chilvers, M., Lux, L., Mueller, D., Shires, M., Webster, R. W., Wise, K. 2026. An Overview of Charcoal Rot of Soybean. Crop Protection Network. CPN-1004. doi.org/10.31274/cpn-20190620-010.