Managing Mid-to Late-season Diseases in Cotton

  • Cotton should be scouted for foliar, wilt, root, and boll diseases from fruiting to defoliation.

  • Management options can be limited for controlling mid- to late-season cotton diseases.

  • Minimizing cotton stress early in the season can help reduce the severity of diseases and help maintain cotton yield potential.


Foliar Diseases


Foliar disease pressure increases when a cotton crop is under stress. Mitigating stress as much as management allows can help protect the yield potential of the crop. Managing irrigation, fertility, insect pressure, and growth can reduce the probability of foliar disease. Rank growth should be controlled through plant growth regulator (PGR) applications and managing water and fertility. Crop residue should be chopped and plowed to accelerate decomposition.1

For more information about foliar diseases, refer to Mid- to Late-season Cotton Leaf Diseases

Target Spot (Corynespora cassiicola)
 Figure 1. Target leaf spot with concentric circles. Figure 1. Target leaf spot with concentric circles.


This disease typically starts in the lower canopy with small reddish spots with light and dark concentric rings.

Diagnostic Notes and Control

Usually occurs after extended periods of leaf wetness. Control rank growth through PGR and water management. Fungicides are available.

Bacterial Blight (Xanthomonas citri pv. malvacearum)
Figure 2. Bacterial blight lesions defined by leaf veins. Figure 2. Bacterial blight lesions defined by leaf veins.


Small, light green, angular lesions on leaves. Bolls with round, water-soaked to brown lesions.

Diagnostic Notes and Control

Resistant varieties are available for most growing regions. Reduce rank growth and consider crop rotation.

Alternaria (Alternaria macrospora) and Stemphylium (Stemphylium solani
 Figure 3. Alternaria leaf spot lesions with purple margins. Figure 3. Alternaria leaf spot lesions with purple margins.


Small, brown, circular lesions on leaves enlarging to 0.4 inch. Old lesions have gray centers. Certain species may cause small purple spots to develop.

Diagnostic Notes and Control

Alternaria is more common in Texas and the Midsouth. Stemphylium is more commonly found in the Southeast. Attributed to potassium deficiency. Fungicides are available.

Cercospora (Mycosphaerella gossypina


Small reddish purple foliar lesions that expand to light brown lesions surrounded by narrow purple margins. Old lesions may be 0.7 inches in diameter. 

Diagnostic Notes and Control 

Plants with moisture and nutrient stress are more susceptible to this disease. Lower yield and fiber quality can occur when part of a disease complex. Fungicides are not considered effective.

Ascochyta Blight (Ascochyta gossypii syn. Phoma exigua)
 Figure 4. Symptoms of Ascochyta blight. Clemson University – USDA Cooperative Extension Slide Series, Figure 4. Symptoms of Ascochyta blight. Clemson University – USDA Cooperative Extension Slide Series,


Small brown foliar lesions that enlarge into irregular dead areas with dark brown borders. Lesion centers may crack and fall out.

Diagnostic Notes and Control

Can occur early in the season and enlarge over time. Usually associated with cool, wet conditions. Fungicide options are available, but generally not warranted.

Wilt Diseases


Fusarium and Verticillium wilts are soil-borne pathogens that can be difficult to manage. The severity of these diseases can be increased by the presence of root-knot, reniform, sting, lance, and lesion nematodes. The disease complex is most well-known with root-knot nematode and Fusarium wilt. Verticillium wilt is widespread across the Cotton Belt with a higher incidence during cool, wet growing conditions.2

Differentiation between Fusarium or Verticillium wilt can be difficult as symptomology of the two diseases are similar. Stem discoloration is typically more evenly distributed with Verticillium wilt. For confirmation of a wilt disease, the lower portion of main stems of cotton plants may be sent to a diagnostic lab. Refer to your local university extension service for sampling procedures.1

Proper fertility management, crop rotation to corn or soybean, use of nematicides, and cotton variety selection can help reduce yield losses from wilt diseases. Nematicides are available for fields with low to heavy nematode pressure. Cotton varieties with improved levels of resistance to Fusarium andVerticillium wilt and Southern root-knot nematode are available to help reduce disease incidence.3

Fusarium (Fusarium oxysporum f. sp. vasinfectum)
Figure 5. Vascular staining caused by Fusarium wilt. Clemson University - USDA Cooperative Extension Slide Series, Figure 5. Vascular staining caused by Fusarium wilt. Clemson University - USDA Cooperative Extension Slide Series,


Wilting and dying plants with adequate soil moisture. Plants may be stunted with interveinal chlorosis. Browning of vascular tissue.

Diagnostic Notes and Control

Most races have a symbiotic relationship with southern root-knot nematode; control nematode populations. Plant varieties with resistance to Fusarium and root-knot nematodes. FOV4 infects cotton independent of nematodes.

Verticillium (Verticillium dahliae)
Figure 6. Irregular leaf mottling found in cotton plants infected with Verticillium wilt. Figure 6. Irregular leaf mottling found in cotton plants infected with Verticillium wilt.


Interveinal yellowing occurs followed by necrosis. Vascular tissue in the stem can become dark. Defoliation can occur.

Diagnostic Notes and Control

Plant tolerant varieties. Residue destruction, weed control, and crop rotation can help.

Cotton Root Rot


Cotton root rot is a fungal disease that is of major economical concern in the southwestern United States. Symptoms begin with leaf yellowing or bronzing followed by wilting at the top of the plant, then at the bottom, and finally complete wilt by the third day. Plants die with leaves secured to the plant. This fungus can survive in the soil for many years; therefore, heavily infected soils may benefit from a three- to four-year crop rotation with a sorghum or corn crop.4

Cotton Root Rot (Phymatotrichum omnivorum)


Rapid wilting of plants in a circular pattern that may quickly lead to plant death. 

Diagnostic Notes and Control

Primarily found in Texas and Arizona. Can rotate to corn and sorghum for three or four years. Deep plowing (6-10 inches), and cereal crop residue can reduce disease pressure. Flutriafol fungicide can be effective.

Boll Rots


Rank growth from periods of warm, humid, and rainy weather as well as excessive nitrogen and/or irrigation applications can lead to boll rots in cotton. Applying a PGR to help control plant growth and increase air circulation in the canopy can reduce boll rots. In areas that are more susceptible to boll rots, wider row spacing and defoliation may also increase air flow. Insect damage can provide an entryway for boll rots into the cotton plant; therefore, controlling mid- to late-season insects may help reduce boll rot damage.2 Boll rots generally appear first as water-soaked brown or reddish-brown lesions on the boll capsule or bracts. The infection can then spread, turning the boll black. Severe infection may cause bolls to fall off the plant.1

Boll Rots (caused by several fungi and bacteria, including fusarium, diploidia, and alternariaspecies)
Figure 7. Boll rot at harvest. Figure 7. Boll rot at harvest.


Small brown to reddish-brown lesions on bolls expand and eventually may turn the entire boll black and dry.

Diagnostic Notes and Control

Avoid practices that result in a rank, dense canopy. Reduce excessive humidity by managing nitrogen, PGR application, and timely defoliation and harvest. Skip row planting patterns can also help manage this disease. 


For more information about wilt, root rot, and boll rots, refer to Mid to Late-season Stem and Boll Diseases in Cotton.


Newman, M.A. 2011. Cotton disease and nematode control. The University of Tennessee Extension.

2 The first 40 days. 2007. National Cotton Council of America and the Cotton Foundation.

3 Wrather, A. and Sweets, L. 2009. Cotton disease and nematode management. G4261. University of Missouri Extension.

4 Texas Plant Disease Handbook. Cotton root rot. Texas A&M AgriLife Extension.



This browser is no longer supported. Please switch to a supported browser: Chrome, Edge, Firefox, Safari.