How Fungal diseases affect Cannabis plants – A guide for beginners

Fungi species can affect the cultivation of cannabis plants in many ways.

Harmful fungi species can cause serious problems for cannabis plants. These fungi can infect the plants and cause diseases, leading to reduced growth, yield, and low quality of the final product. The fungi species that are considered harmful are the ones that rot, decompose, and damage the Cannabis plant. They can appear in the leaves, roots, stems, and flowers. 

Beneficial fungi species can help plants to grow healthy by increasing nutrient availability, protecting against pests and diseases, and improving soil structure. For example, beneficial fungi species like Mycorrhizae and Trichoderma harzianum can protect the plant against harmful fungi species.

Cannabis plant suffering from root rot
Cannabis plant suffering from root rot

In this article, you’ll learn about some common harmful fungal species that cause diseases in cannabis plants, their effects, and how to manage them to grow healthy plants. You’ll find some photos and pictures of plants with all kinds of fungal diseases and how they show on each part of the plant.

First, this is how a healthy plant looks in the vegetative stage. The leaves are green and growing with vigor. There are no signs of fungal infections or diseases.

Healthy cannabis plant
Healthy cannabis plant

How to group fungal diseases: by plant part and tissue

Scientific research suggests that diseases and pathogens are best grouped by the tissue they affect1. Here are some examples:

On the roots: these fungi include several species of Fusarium, which cause brown discoloration of the roots and stem. Plants with root rot look yellow and stunted. Fusarium can kill plants quickly.

On leaves and stems: Powdery mildew is one of the most common fungi found in cannabis crops. It appears as a white or gray powder on the leaves and stems of the plant.

On flowers or buds: Many species of fungi grow on flowers, during the flowering stage. Penicillium bud rot, Botrytis bud rot, and Fusarium bud rot are very common on cannabis plants. Botrytis can also spread on harvested buds and damage the entire yield.

Inside the plant: Endophytic fungi are fungi that occur in the plant tissue and do not cause any obvious symptoms.

This illustration from another research study shows many diseases and their location in the cannabis plant.

The emerging pathogens on cannabis and hemp plants.
The emerging pathogens on cannabis and hemp plants. Pathogens shown in bold are the most damaging.
Source: Emerging diseases (cited at the bottom)2

How to prevent Fungal diseases and infections in indoor cannabis plants

Below are some preventive measures you can use to create your own simple yet effective Pest Management or pest control system according to your growing space and possibilities.

  • Monitor your plants regularly for signs of fungal infections and watch for wilted leaves and stunted growth. Watch for symptoms to identify the disease and treat your plants.
  • Good hygiene practices are key to preventing the spread of the fungus. This includes cleaning and sterilizing your grow room, tools, and containers.
  • Wear gloves when handling plants and harvested buds. Clean gloves regularly and between plants if you suspect a fungal infection.
wear gloves cannabis infection preventive fungi
Wear gloves and clean gloves and tools between plants
  • Control the humidity levels in your grow tent or room. Many fungi species thrive in high humidity, so keep a relative humidity of around 50%, especially during the flowering stage. Use a humidifier or dehumidifier to help regulate humidity.
  • Provide good air circulation. Poor air circulation can worsen many fungal diseases, so make sure your grow room has good ventilation.
  • Use resistant cannabis strains. Some cannabis strains are more resistant to fungal diseases than others. Learn which ones are adapted to the environmental conditions in your area and are less susceptible to infection.
Cannabis plants with good ventilation and clean environment
Cannabis plants with good ventilation and a clean environment

  • Use preventative measures such as neem oil, silica, Trichoderma, and horsetail foliar applications to help prevent fungal development. These products can be sprayed on the leaves and stem of the plant and also in the root system as part of a nutrition schedule. Always scout your plants for pests and diseases. In this article, you’ll get information on which to use for each disease and how to apply each treatment.
  • Remove and destroy infested plants or plant parts if you do notice an outbreak of fungal disease. This will help you prevent the spread of the fungus to healthy plants.
  • Use a fungicide specifically formulated to control the fungus causing the infection. Follow label directions carefully and reapply as needed to keep the fungus under control. Make sure that the fungicide is approved for use on cannabis and will not harm people, animals, or pollinator insects if growing outdoors.
  • Chemical fungicides can harm people and the environment, Use caution and wear protective clothing when applying them and consider using organic or natural alternatives.
  • Monitor and control fungal infestations in other crops near your cannabis crop. Many species of fungi can come from neighboring fields or house plants and infect your cannabis plants. Some crops that can carry Botrytis and Fusarium are tomatoes, blueberries, barley, and garlic.
Lesions on Cannabis leaves caused by Botrytis Cinerea2
Lesions on Cannabis leaves caused by Botrytis Cinerea2

Common fungi diseases that can attack cannabis plants:

Damping-off (Seedling or cutting stem): Damping-off is a common disease that can affect cannabis seedlings, cuttings, and young plants. In seedlings, the stem weakens and gets thinner until the seedling dies. Caused mainly by two different fungi: Pythium and Fusarium.

Damping off disease in cuttings
Damping off disease in cuttings. Source: Pathogens and molds1

Fusarium (Roots and stem): This fungus rots the roots and lower stem of the plant, often leading to stunted growth or death. It is often caused by overly wet or poorly drained soil.

Fusarium causes yellowing of the leaves. fungi
Fusarium causes yellowing of the leaves. Source: Emerging diseases2

Powdery mildew (leaves): This is a fungal disease that appears as a white or gray powder on the leaves and stems of the plant. Powdery mildew weakens the plant and it can cause low-quality yields.

powdery mildew fungi cannabis plant
Powdery Mildew – Source: Pathogens and molds2

Botrytis cinerea (flowers or buds): This fungus can infect the flowers and leaves of the plant, leading to necrosis (death of plant tissue). High humidity levels and poor air circulation helps Botrytis spread quickly.

botrytis cannabis flower and leaves
Botrytis causes bud rot. Source: Emerging diseases1

Let’s analyze these fungi diseases one by one:

Damping-off disease in cannabis seedlings

What is damping-off

Damping-off disease is a common problem that can affect cannabis seedlings and young plants. The seedlings suddenly seem debilitated and die. The damping-off disease is most commonly found in damp soil mixes with poor aeration.

How to identify damping-off

The collapse of the seedlings: The seedlings may suddenly collapse or die, often before they have had a chance to develop into mature plants.

Stunted or deformed growth: Damping-off disease can cause the seedlings to grow poorly or deformed. The stem thins out and the seedling falls off. 

Yellow and wilting leaves: As the fungus or bacteria spreads, it can cause the leaves of the seedlings to wilt or turn yellow.

seedling damping off fungi infectiom
Seedling with damping off disease

How to prevent damping-off

Use clean soil and water slowly to avoid overwatering. Use a clean growing medium with good aeration and avoid pots with poor drainage. Maintaining proper ventilation and temperature levels can also help to prevent the spread of the fungus or bacteria.

damping off fusarium cuttings cannabis fungi
Damping off in cuttings caused by Fusarium with no treatment
Source: Emerging diseases

How to manage damping-off

There’s a big chance that an already infected seedling won’t recover. It’s better to remove them immediately from the growing room and discard them in a sealed bag. In this case, the most important thing is to prevent the spread of the disease to other seedlings. Again, good hygiene practices and sterilization protocols help avoid spreading the disease.

Reduce ambient relative humidity, and improve air circulation. Use fans, air-conditioned, dehumidifiers, and exhausts to improve air circulation.

Removed diseased cuttings as soon as you find out. Dispose of them in a closed bag and take them out of the grow room.1

Apply biological control agents like Trichoderma Harzianum at the rooting stage.

cuttings with fusarium fungi cannabis
Cuttings inoculated with Fusarium without treatment (left) and with Trichoderma sp. (right) after 14 days.
Source: Emerging diseases1


What is Fusarium

Fusarium is a family of fungus that attacks cannabis plants and cause significant damage. Fusarium grows mostly in the soil and it can live there for a long time. It can also be transmitted through cuttings and even seeds. Fusarium is most common in young plants or seedlings, but it can attack plants at any stage. Some Fusarium species cause damping-off and also root and bud rot.

cannabis plant infected with fusarium pythium fungal infection
A plant in the field infected with Fusarium and Pythium
Source: Pathogens and molds2

How to identify Fusarium

Fusarium appears mostly in indoor crops and live in the growing medium. When fusarium attacks, it rots the stem base of the seedling or grown plant. Older leaves show signs of yellowing. The soil is damp and smells of rot.

cannabis plant fungi fusarium
Healthy plant (left) and plant infected with Fusarium spp. (right).
Source: Pathogens and molds2

How to prevent Fusarium

Keeping the grow space clean. The key to preventing Fusarium infestations is to keep the growing space clean and free of dead plants and infected plant material.

Ensure good air circulation. Poor air circulation can contribute to the spread of Fusarium, so make sure your grow room is well-ventilated.

Use sterile soil and containers to prevent the spread of the fungus.

Avoid overwatering and ensure that the soil has good drainage. Fusarium thrives in wet, poorly drained soil.

Avoid damaging the roots when transplanting. Be careful and wear gloves when touching the roots in the process.

Inoculating the substrate with Trichoderma harzianum will help the plant, as it is an antagonistic fungus.

cannabis roots stem fungi fusarium pythium
Visible mycelial growth of Fusarium infecting roots and stem
Source: Pathogens and molds2

How to manage Fusarium

Monitor your plants regularly for signs of fusarium, such as yellowed or wilted leaves and stunted growth. Also, check the roots as well, some plants may be saved by pruning the infected root parts, but there’s a chance that the fungus will spread again.

Improve drainage: Overwatering or poor drainage can create ideal conditions for Fusarium to thrive. To help contain the spread of the fungus, it is important to improve soil drainage and avoid overwatering. Choose aerated soil mixes and containers with good drainage.

Disinfect tools and equipment: Fusarium can be transmitted through contaminated tools and equipment. If you suspect a plant is infected, disinfect all tools before moving on to the next plant to avoid spreading the fungus.

cannabis plant fusarium fungi rot
Symptoms of plant collapse as a result of infection by Fusarium.
Source: Pathogens and molds2

Improve growing conditions: Fusarium thrives in warm, moist conditions. To control the spread of the fungus, it is important to maintain proper growing conditions, including adequate ventilation and temperature levels.

Test mother (stock) plants to ensure they are disease‐free.

Avoid injury to roots, stems, and overwatering. Fusarium can also affect the stems.1

stem rot necrosis fusarium fungi
Internal stem necrosis caused by Fusarium. Source: Emerging diseases.1

Powdery Mildew

What is Powdery Mildew

Powdery mildew is a common fungal disease that affects many plants, including cannabis. It can spread quickly in high humidity and poor ventilation.

Powdery mildew feeds on the nutrients and water in the plant. As it grows, the plant has difficulty photosynthesizing and absorbing nutrients. This leads to poor growth, lower yield, and poor quality of flowers

powdery mildew fungal infection cannabis
Powdery mildew on leaves and stems
Source: Pathogens and molds2

How to identify Powdery Mildew

Powdery mildew first shows up as small patches of white or gray powder (like flour) on the top of the leaves and then grows on the stems and buds. Powdery Mildew may resemble pollen, dust, or even trichomes on the leaves, but if you look closely with a hand lens or magnifying glass, you can see the fuzzy-looking fungi growing.

White or gray powder on the plant: The most common symptom of a powdery mildew infection is the white powder on the leaves. 

Yellow and wilting leaves: When infected with powdery mildew leaves begin to wilt or turn yellow.

Stunted growth: A plant infected with Powdery Mildew may stop growing or grow more slowly than usual.

powdery mildew leaves cannabis plant fungi
Plant infected with Powdery Mildew. Source: Emerging diseases1

How to prevent Powdery Mildew

Watch your plants for signs of powdery mildew, such as white or gray powder on the leaves.

Control the humidity in your grow tent or room. Powdery mildew spreads quickly in enclosed spaces with high humidity. Keep a relative humidity of around 50%. You can use a humidifier or dehumidifier to help regulate humidity n your room or tent.

fungi powdery mildew cannabis plant
Macro photo of a leaf infected with Powdery Mildew

Foliar application of silica or potassium silicate on the plant and in the growing medium from the beginning. Use the manufacturer’s recommended levels as there are many different concentrations and they will affect the pH. Silica is not an essential element but it’s highly beneficial for Cannabis. Silica inhibits the development of Powdery mildew.

Some treatments recommended for powdery mildew prevention and management are:

  • Vegetative cuttings should be disease‐free
  • Grow strains that are tolerant to infection
  • Remove and destroy diseased leaves1

How to manage Powdery Mildew

Powdery Mildew is a fungal disease that has to be treated from different angles at the same time. Treating the plant with one only treatment won’t work as the fungi rapidly develop resistance and it gets harder and harder to eliminate. The best idea is to combine some pest management treatments and closely inspect our plants periodically.

cannabis leaf powdery mildew
Cannabis leaf severely infected with Powdery Mildew. Source: Emerging diseases1

Foliar sprays with different active ingredients can help control Powdery Mildew. Be sure to spray the entire leaves and stems rather than the flowers. Here are some options:

Foliar applications of Equisetum Arvense L (Field horsetail) twice a week, in water solution. Use as recommended by the manufacturer.

cannabis plant foliar application preventive fungi
Cannabis plant with foliar application of preventive products

Treatments applied weekly for 4 weeks:

Here are some commonly recommended treatments. Read the source (Emerging diseases2) to see the exact treatment applied in these cases.

1- Untreated control leaf with Powdery mildew.

powdery mildew cannabis leaf no treatment
Leaf infected with Powdery Mildew without treatment
Source: Emerging diseases 2

2- Foliar applications of water and potassium or sodium bicarbonate solutions.

powdery mildew on cannabis plant potassium bicarbonate
Leaf treated with Potassium bicarbonate
Source: Emerging diseases 2
  • You can start by mixing 1 tablespoon of baking soda in a gallon of water (3.78 L) and spraying the leaves and stems. Better use in the vegetative stage once a week.

3- Foliar application of hydrogen peroxide (H2O2) and water solutions.

cannabis leaf powdery mildew fungi hydrogen peroxide
Leaf treated with Hydrogen Peroxide
Source: Emerging diseases 2
  • You can start by mixing one tablespoon of hydrogen peroxide in a gallon of water (3.78 L) and spraying the stems and leaves once a week.

4- Leaves received daily exposure to UV‐C for 3–5 s over 28 days. Be extra careful and follow the manufacturer’s instructions to apply if using this method as it can be damaging to humans.

leaf uvc light cannabis powdery mildew
Leaf treated with UV-C light
Source: Emerging diseases 2


What is Botrytis

Botrytis cinerea is a common type of fungus that affects cannabis plants. Botrytis can attack the plant while it is still in the flowering stage and cause entire branches or even the whole plant to rot if it’s not trated properly.

botrytis on cannabis flower
Close-up of flowers infected with Botrytis

Botrytis can also be found as a post-harvest mold on flower buds if the drying and curing conditions are not optimal or if the plant was infected at harvest time. Wear gloves when trimming and avoid touching infected flowers with the same gloves or disinfect them after touching flowers with mold.

gloves trimming cannabis fungi
Wear gloves during trimming to avoid spreading fungal infections

Smoking or eating cannabis infested with Botrytis is bad for your health, just throw away the infested parts.

How to identify Botrytis

Fuzzy brown or gray fungus on the buds: Botrytis cinerea infection shows mainly inside the densest and largest flower buds.

botrytis cinerea cannabis bud
Cannabis flowers with Botrytis growing. Discard these flowers.

Yellow, brown, and wilting leaves: Leaves wilt or turn yellow, and brown, and then die as Botrytis spreads. 

early infection botrytis fungi cannabis
Early infection of Botrytis on flowers and leaves. Source: Pathogens and molds2

Stunted growth: Plants infected with Botrytis show stunted and slow growth.

How to prevent Botrytis

Look for signs of fungal infection such as brown or gray patches or spots on the leaves and stems of your plants.

Keep the area clean to prevent the spread of the fungus. This includes cleaning and sterilizing your growing room, tools, and containers.

cannabis flower botrytis bud rot
Bud rot caused by Botrytis

Control the humidity in your grow room or tent. Botrytis grows when humidity is high, so try to keep a relative humidity of about 50%, especially during the flowering stage. It is a good idea to use a humidifier or dehumidifier to help regulate humidity.
Provide good air circulation. Poor air circulation can favor the development of Botrytis, so make sure your grow room is well-ventilated.

botrytis bud rot fungi
Botrytis bud rot development, caused by Botrytis cinerea. Source: Pathogens and molds2

Some specific preventive treatments for Botrytis include

  • Use biological control agents at rooting, such as Trichoderma (beneficial fungi). 
  • Avoid growing strains with large dense colas indoors in humid conditions as they retain moisture better than loose buds.
  • Reduce humidity and moisture to 50% during the flowering stage
  • Avoid damage to buds during harvesting and trimming
  • Cut out and destroy diseased buds1

harvested buds botrytis cannabis
Close-up of diseased harvested flowers. Botrytis can continue to infect flowers after harvest. Discard infected buds. Source: Pathogens and molds.2

How to manage Botrytis

Cut or prune the infested part, and throw it away. There’s no single treatment that works alone, it’s better to combine several preventive methods as a part of Integrated Pest Management.

Advanced stages of bud rot caused by Botrytis.
Source: Pathogens and molds2

Take away

To prevent the spread of harmful fungi and promote the growth of beneficial fungi in cannabis cultivation, provide proper growing conditions and take steps to control the spread of disease. 

This may involve using sterilized soil and filtered RO water, maintaining proper ventilation and temperature levels, and applying fungicides or other control measures.

Regularly checking the plants for signs of infection and taking steps to control the spread of harmful fungi can help to protect the plants and ensure a healthy crop.

healthy plants cannabis flowering
Healthy Cannabis crop in the flowering stage

Use the Grow with Jane app to monitor your plants regularly and log any changes. You can take and keep notes, and photograph infected tissue as soon as you notice it to track its progress. Planning and logging all the treatments you apply with notes and measurements will help you organize your pest management system. In future crops, you’ll be able to detect earlier when something is not going as planned and use past information to prevent or treat new diseases.

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Citation of sources

1 Punja ZK, Collyer D, Scott C, Lung S, Holmes J and Sutton D (2019) Pathogens and Molds Affecting Production and Quality of Cannabis sativa L.. Front. Plant Sci. 10:1120. doi: 10.3389/fpls.2019.01120

2 Punja ZK. Emerging diseases of Cannabis sativa and sustainable management. Pest Manag Sci. 2021 Sep;77(9):3857-3870. doi: 10.1002/ps.6307. Epub 2021 Feb 27. PMID: 33527549; PMCID: PMC8451794.

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