Several organisms cause root rot in cannabis. The main ones are the water moulds of the Pythium group, some of which have been renamed Globisporangium, and the true fungi Fusarium and Rhizoctonia [1]. They live in the root zone, and by the time leaves wilt the roots are already badly damaged. Fusarium cannot be cured once it is inside the plant, so prevention does most of the work. This part covers how to prevent root disease, how to respond to an outbreak, the extra pressure in hot and wet Southeast Asian conditions, and a routine for checking root health.
This is Part 2. Part 1: Root Rot, Pythium & Fusarium: Protecting Cannabis Root Systems
1. Prevention
1.1 Water temperature and oxygen in hydroponic systems
Warm water holds less dissolved oxygen, which is oxygen gas mixed into the water. Roots that are short of oxygen stop defending themselves. Pythium’s swimming spores (zoospores) are also most active in warm water. Keeping the reservoir cool therefore prevents most Pythium outbreaks in hydroponics.
- Keep the reservoir at 18–22 °C. In this range the water holds more oxygen for the roots, and the pathogen is slower.
- Use a water chiller, a unit that cools the nutrient solution, when room conditions push the water above this range.
- Run air pumps and airstones. Aim for dissolved oxygen above 6 mg/L, measured with a dissolved oxygen meter. This keeps roots supplied and able to defend themselves.
- Check the water temperature every day. A single hot weekend can start an outbreak that you only see weeks later.
Translator’s note: at Thai room temperatures of 30–35 °C, a reservoir without a chiller stays warm and low in oxygen. A chiller lets you control the setting behind most Pythium outbreaks. Include it in your budget before you buy tents and lights. To start, log reservoir temperature twice a day for two weeks, then size the chiller to the highest reading. The topic on running hydroponics at 31 °C reservoir temperature compares chillers with the other options.
Translator’s note: chillers and air pumps both stop during a power cut, and in many parts of Thailand cuts happen during storms. Put the air pump on a UPS (uninterruptible power supply, a battery unit that keeps a device running during a cut), or keep a battery-powered air pump ready. A thermometer that records the day’s highest reading shows whether the water overheated while you were away. After any power cut, check the water temperature and the reservoir smell the same day. This lets you act before the roots start to rot.
1.2 Drainage and watering
- Aim for 15–20% runoff in soil and coco. Runoff is the water that drains out of the bottom of the pot, as a share of the water you gave. It refreshes the solution around the roots and prevents salt build-up. Measuring the EC and pH of the runoff also tells you what is happening in the root zone.
- Let the top layer dry between waterings. Constant wetness suffocates roots.
- Use fabric or air-pruning pots. They let air into the root zone and let excess water out.
- Raise pots off the floor and never let them stand in water.
What to do: for one week, measure how much water drains out compared with how much you give. Adjust the volume until you reach 15–20%.
1.3 Beneficial microbes
Some microbes live on roots and protect them. These products contain them.
| Organism | Example products | What it does |
|---|---|---|
| Trichoderma harzianum | RootShield, Trianum, Great White | Colonises the root surface and works against root pathogens |
| Bacillus subtilis | Serenade, Cease | Produces antibiotic compounds (lipopeptides) |
| Bacillus amyloliquefaciens | Double Nickel, Hydroguard | Colonises the root zone; some formulations are made for hydroponics |
| Mycorrhizal fungi (AMF, arbuscular mycorrhizal fungi) | Mykos, Great White, Dynomyco | Live in partnership with roots, improving uptake and plant vigour |
| Clonostachys rosea (formerly called Gliocladium catenulatum) | Prestop | Works against pathogens in the growing medium |
Apply them at transplant, directly onto the root ball, and reapply as the label directs. Do not combine them with hydrogen peroxide or chlorine treatments. These sterilants kill the beneficial microbes along with the pathogens, so you pay for both and keep neither.
Biological control of cannabis root pathogens is still being researched, not a solved problem. Results vary with the product, its formulation, the growing medium and the pathogen. Use microbes as one layer, on top of temperature control, oxygen, drainage and sanitation. They do not replace those basics.
Translator’s note: the products in the table are mostly made in the United States and Europe. We could not confirm which of these products, or which Thai-made Trichoderma and Bacillus products, are registered with the Department of Agriculture and sold in Thailand. To find a product, ask the official distributor in Thailand, or ask other growers in the Fungi and Mycology section. Start with a small trial. Treat one batch of plants and leave one batch untreated under the same conditions. Then compare root colour and the number of sick plants at harvest, so you know whether the product earns its cost in your room.
1.4 Clean growing media
The handbook’s advice on hemp root rot is almost entirely about growing practice, and it is specific [1]:
- Use clean pots and sterile growing media.
- Keep the amount of organic matter in the planting medium low.
- Disinfect tools and equipment.
- Never reuse potting soil from diseased plants.
The handbook gives no chemical control recommendations for hemp root rot [1]. In practice, this means the disease has to be prevented, because no spray is recommended to cure it.
1.5 Sanitation
- Disinfect pots, trays and tools between crops. Soak them for 10 minutes in a 10% bleach solution (1 part household bleach to 9 parts water), then rinse thoroughly.
- Drain, scrub and rinse reservoirs between crops.
- Remove dead plant material promptly. Dead tissue becomes a new source of spores.
- Put a foot bath at the room entrance. It stops contaminated soil from being carried in on shoes.
What to do: write a cleaning checklist for the end of every crop and tick off each item before the next planting.
2. Responding to an outbreak
2.1 Pythium in hydroponics
- Bring the reservoir temperature down to 18–20 °C.
- Raise dissolved oxygen by adding airstones and pump capacity.
- Change the reservoir. Drain it, clean it and refill it.
- Use hydrogen peroxide only as an emergency measure. It kills zoospores in the water, but it also kills your beneficial microbes. Use it once, at the dose on the product label, not as a routine.
- Add beneficial microbes again 24–48 hours later. This rebuilds the biology you just removed.
- If the problem keeps coming back, change to a system with better oxygen supply. Recirculating deep water culture (RDWC) connects several root buckets to one central reservoir. With external pumps and a chiller, it tolerates pathogen pressure far better than single, unconnected buckets.
See hydroponic systems compared for how the systems differ.
2.2 Pythium in soil or coco
- Water less often. Let the medium dry further between waterings.
- Improve drainage. If the mix holds too much water, add more perlite.
- Drench the medium with a Trichoderma or Bacillus product.
- Potassium phosphonate (also sold as phosphorous acid; products include ProPhyt, Fosphite and Agri-Fos) is one of the few chemical options that works against oomycetes. Roots absorb it. Before using it, check whether it is registered for cannabis and what residue rules apply. A product permitted on ornamental plants is not automatically permitted on a crop that people consume.
Translator’s note: in Thailand, use only products registered with the Department of Agriculture (กรมวิชาการเกษตร), and use them only as the label directs. We could not confirm that any potassium phosphonate product is registered with the Department of Agriculture for use on cannabis or hemp. See what you may legally spray under Thai GACP before you buy.
2.3 Fusarium
Once Fusarium is inside the plant’s water-carrying tubes (xylem), no reliable cure exists. A drench poured into the pot cannot reach the fungus there.
- Remove and destroy badly infected plants. Put them in sealed bags. Do not compost them.
- Try to save a plant only if its genetics cannot be replaced. Take it out of the contaminated medium and trim off the dead roots. Drench it with a Trichoderma product and replant it in fresh, sterile medium. Success against vascular wilt (wilt in the water-carrying tissue) is poor, so treat this as a last attempt, not a standard method.
- Stop the spread. Disinfect every tool that touched the plant, and take the contaminated medium out of the building.
- For the next crop, use fresh medium, never the old one.
Translator’s note: licensed growers in Thailand may have to record how they destroy cannabis plants. Ask your licensing office before you dispose of infected plants, so the disposal matches your records.
3. Why root disease pressure is higher in Southeast Asia
Growers in Southeast Asia face more root disease for three reasons. High air temperatures push up the temperature of reservoirs and growing media. Heavy monsoon rain waterlogs outdoor ground. High humidity slows the plant’s water loss through its leaves, so the medium stays wet for longer.
- In hydroponics, treat a water chiller as a core part of the system. At 30–35 °C room temperature, a reservoir without a chiller stays in the warm, low-oxygen state these pathogens need. Budget for it before the tents, not after the first failed crop.
- Outdoors, plant in raised beds or mounds. A week of rain then drains away instead of leaving roots in standing water. See outdoor cannabis in Southeast Asia.
- Add beneficial microbes more often than temperate-climate guides suggest. Tropical heat speeds up the beneficial organisms as well as the pathogens. A single application at transplant protects the roots less well here than in a temperate greenhouse.
- For container growing, choose coco over heavy tropical soil. Coco drains and lets air into the root zone much better.
- Use shade cloth on outdoor crops during the hottest period to keep the root zone cooler.
- Do not rely on a mildew spray programme against Fusarium. In a 2025 laboratory test on the Fusarium that caused bud rot in a Chiang Mai hemp greenhouse, sulfur stopped only 11% of fungal growth [2]. Sulfur is a tool for mildew, not for Fusarium.
What to do: before the rainy season starts, check that every pot and bed drains freely and that your reservoir can be held at 18–22 °C.
4. A routine for checking root health
| Check | How often | What to look for |
|---|---|---|
| Pot weight | Daily | A pot that should be light but is still heavy shows a drainage problem |
| Roots | Weekly, on plants that look weak | Colour, texture, smell |
| Reservoir smell | Daily (hydroponics) | Any sour or swampy smell means trouble |
| Dissolved oxygen | Weekly (hydroponics) | Above 6 mg/L |
| Water temperature | Daily (hydroponics) | 18–22 °C |
| Growth rate | Ongoing | A sudden slowdown with no other explanation means you should check the roots |
| Runoff EC and pH | Every watering | Sudden changes can mean the roots are taking up less |
What to do: print this table, keep it in the grow room and record the readings in your grow log. When a plant falls sick, you can then see when the trouble started.
5. Root health checklist
- Temperature control: a chiller in hydroponics; shade and airflow for soil grows in hot climates.
- Drainage: fabric pots, enough runoff, no standing water.
- Beneficial microbes: at transplant, then on a schedule.
- Dissolved oxygen: airstones in hydroponics, an open, airy mix in soil.
- Sanitation: clean pots, tools and reservoirs between crops.
- Monitoring: water temperature every day, and a weekly root check on a few typical plants.
- Emergency plan: for sudden Pythium, use peroxide, change the water and add microbes again; for Fusarium, remove and destroy the plants.
Expensive nutrients, perfect lighting and advanced plant training cannot make up for damaged roots. Spend money and time on temperature control, drainage and sanitation first. For a wider pest and disease approach, see integrated pest management for cannabis.
If you have dealt with root rot, describe it below this topic. Say which system you use (hydro, soil or coco), which organism you suspected or confirmed, what you did and what happened. Questions are welcome too.
References
- Osterbauer, N.K., & Ocamb, C.M. Hemp (Cannabis sativa)-Root and Crown Rot. In: Pacific Northwest Plant Disease Management Handbook. Oregon State University, Washington State University and University of Idaho Extension (revised March 2026). Hemp (Cannabis sativa)-Root and Crown Rot | Pacific Northwest Pest Management Handbooks
- Samarakoon, M.C., Chiu, C.-I., Chobyen, J., Iamwan, S., Bundit, A., Jeeatid, N., & Mukjang, N. (2025). Fusarium pernambucanum causing bud rot in industrial hemp (Cannabis sativa) in Thailand: pathogenicity and sensitivity to fungicide in vitro. Physiological and Molecular Plant Pathology.
This article is part of the Asiannabis Community series on pest and disease management. It is for education in places where cannabis cultivation is legally permitted. For which licence covers which activity in Thailand, see Licensing and Compliance in Thailand.