Identifying and Dealing with Alternaria on Cannabis Plants

By Chris Bond
Published: February 21, 2023 | Last updated: February 21, 2023 11:04:16
Key Takeaways

Difficult to diagnose, Alternaria is a nasty fungal pathogen when it gets into a cannabis crop. It’s very difficult to treat and some forms can kill a plant or entire crop within hours. Preventing Alternaria is a grower’s best defense but some treatments will work as well.

Alternaria is one of the most common genera of fungal pathogens that affect cannabis crops, as well as numerous other agricultural and ornamental crops around the world. Some estimates place Alternaria as responsible for as much as 20 percent of all agricultural crop losses due to disease. Because it can travel via several modes, Alternaria can very easily prey upon your cannabis plants. It can be airborne, be introduced to crops through infected soil, or be carried in water via irrigation, splashed onto leaves or soil and spread from plant to plant.

Alternaria starts out as a seed-borne fungus. Once a cannabis plant from an infected seed germinates and develops, the disease is transferred into the host plant, and then can infect any nearby plants as well. The disease is slow to develop, and as such affected plants do not often show symptoms until they are mature, even well into the flowering stage.

Because Alternaria can be carried by multiple host species besides cannabis, marijuana plants growing near other crops can be susceptible even if grown from certified clean seed. Common agricultural crops like carrots, potatoes, beans, tomatoes, and herbaceous plants can harbor this disease and spread it to nearby cannabis crops. Most types of Alternaria present as lesions on leaves or stems. There are some forms however, that can cause cannabis plants to develop sudden root rot which can kill single plants or even entire crops within a matter of hours. Fortunately, this species of the disease is not as common as the version that causes leaf spots.


Symptoms of Alternaria

leaf of a cannabis plant infected with Alternaria

It can be difficult to diagnose Alternaria on cannabis as its symptoms can look like those of many other diseases. It is most often mistaken for Botrytis, or other common fungal pathogens. Alternaria often first appears as purple to brown leaf spots about three-quarters of an inch (2 cm) in size. Sometimes there are further black spots on top of these purple-brown spots. These black spots contain the spores of the fungal disease. Sometimes the margins of the purple-brown spots are yellow. The spots tend to be oval or irregularly shapes and can appear in concentric rings like the rings of a bull’s-eye target.

When the spots are on leaf veins, the attached leaf will become distorted and yellow overall, before ultimately succumbing to the disease and falling off. Lower, older leaves are generally the first to show signs of this infection. Alternaria spots can appear on the stems as well. These spots are longer than those on the leaf, generally greater than one inch long. They also are often sunken or concave in appearance. When these lesions form at the base of the plant, at the soil line, they can girdle and kill the cannabis plant. These are not the only symptoms that can accompany an infestation of Alternaria, however.

Necrotic (dead) spots can appear anywhere on an affected plant, not just leaves and stems. They can appear on parts of the flower too, on petioles and bracts. This disease can also cause less obvious symptoms such as slowed or stunted plant growth. It can reduce the host plant’s ability to absorb nutrients appropriately. This can of course result in a wide range of other deficiencies and problems, many unseen, which can make positive identification of the disease even more difficult since there can be many non-fungal causes of poor nutrient absorption in a plant.


Treating Alternaria

Alternaria is not an easily treated disease of cannabis (or any other type of crop). In general, once a plant has it, it is extremely difficult to control and, in most cases, the affected plant(s) should be destroyed, as well as any leaves, flowers, or branches that may have fallen off of it. If Alternaria is undetected once cannabis plants have entered the flowering phase, control of the disease is all but impossible. Until that point though, there are a few options.

If pesticidal controls are desired to attempt to remediate the disease, there are a few possible fungicides that can be tried. For those wanting an organic option, fungicides containing copper (if labeled for organic use) should be tried. It must be labeled specifically for organic production for those growers who are producing certified, clean cannabis crops. For those not looking for organic solutions, there are additional options.

Captan is a fungicide that has been used with success for decades on a variety of fungal pathogens. Chlorothalonil is another reliable standby. Additionally, fungicides containing either active ingredient trifloxystrobin or triflumizole can be used as a treatment as well. As with any fungicide, strict adherence to the directions for use on the label are critical for best results and the use of appropriate personal protective equipment (PPE) should not be seen as optional, but as a requirement to use each respective pesticide responsibly and legally. None of these options should be expected to provide 100 percent control of the disease but can help to reduce its spread if caught early enough and applied according to directions.

Preventing Alternaria

Grower removing the leaves of an infected plant

Alternaria, like most fungal infections, develops in particularly humid (above 80 percent), warm (over 60°F/15°C), and moist conditions. When Alternaria spreads onto a cannabis plant’s leaves, what would normally be ideal conditions for plant growth, can contribute to the disease’s rapid spread and development. Morning dew, coupled with the day’s humidity and warmth will help spread the spores of the disease across the plant’s leaves and stems. Within half a day, the disease can penetrate the plant, colonize, and start reproducing and spreading to other neighboring plants, unnoticed to even trained disease scouts.

There are other factors besides weather and environmental conditions that can make your cannabis plants particularly prone to the disease’s introduction and development. Poor soils and bad nutrient management invite Alternaria as well. Decaying matter and diseased crop debris are also where this disease often develops and breeds before infecting plant hosts. Good crop management practices, including the complete removal or destruction of the prior year’s roots, stems, and other spent biomass are critical steps in trying to combat the spread of this common fungal disease.


As with all plant diseases, the best way to treat Alternaria is to never get it to begin with. Sanitation throughout all phases of cannabis cultivation is a must to control this and most other plant diseases. Start by procuring seed that is certified as being disease-free. If that is not possible, then at least treat your seed with a hot water (about 120°F/49°C) bath for about 20 minutes. This will kill some of the potential pathogens on the seed without sterilizing the seed. Only do this for seeds that are not otherwise treated.

When you are ready to seed, use only fresh soil media. If growing outside, make sure you are not planting into soil with decomposing matter from a previous crop. Space your seeds or transplants far enough apart so there is good air circulation around each plant. When growing inside, make sure there is enough, proper ventilation with steady temperature and humidity levels.

Make sure not to overwater or get water on the leaf surfaces. Water the soil, not the leaves, and let it get slightly dry in between waterings. Whenever possible, water early in the day so that excess moisture can evaporate and not begin to harbor fungal pathogens.

Keep all debris, compost, and cull piles far away from your developing crops. It is easier than you might think for pathogens to jump from one area to another without even realizing it until it is too late. Keep weeds near your crops under control. Pathogens can just as easily be on weeds and transfer to your crops as they can be on cannabis plants.

The bottom line on prevention is that you can’t be too careful about keeping your growing environments as clean and sanitary as possible. This will help to eliminate the chances of developing Alternaria on your crop, but also many dozens of other unwanted pathogens as well.


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Written by Chris Bond | Certified Permaculture Designer, Nursery Technician, Nursery Professional

Profile Picture of Chris Bond

Chris Bond’s research interests are with sustainable agriculture, biological pest control, and alternative growing methods. He is a certified permaculture designer and certified nursery technician in Ohio and a certified nursery professional in New York, where he got his start in growing.

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