How to Treat 13 Common Garden Fungal Diseases

Notice fuzzy white mold on your plant’s stems or dark spots on their leaves? A fungus could be the culprit. Join plant enthusiast Briana Yablonski as she covers 13 common fungal diseases to look out for in your garden.

downy mildew fungal diseases on cucumber leaves


Even if you provide your plants with the proper environment and care, diseases can still infect them. Fungal diseases can cover your plants with layers of fuzz, lead to rotten fruits, and even kill plants. But how do you know which disease is to blame?

Learning the different symptoms of common fungal diseases helps you correctly diagnose the disease. Proper diagnosis allows you to enact prevention strategies and help keep the disease from spreading.

Join me as I cover 13 of the most common garden fungal diseases, including wilts, mildews, and leaf spots. I’ll share how to identify, prevent, and treat each disease to help you keep your plants healthy.

Fusarium Wilt

Close-up of sunflower plants affected by Fusarium Wilt, in the garden. Sunflower plants affected by Fusarium Wilt exhibit wilting and yellowing of their leaves, stunted growth, and a general decline in overall health. The leaves of the plant are curled, wilted, drooping and have brown-orange spots.
Early signs include wilting leaves, sporadic yellowing, and reddish-brown plant stems.

Fusarium wilt is caused by fungal pathogens in the Fusarium genus. This genus has various forms, each attacking a specific host plant. Some plants commonly affected by Fusarium wilt include tomatoes, peppers, eggplant, and basil


One of the first signs of Fusarium wilt is limp and wilted leaves. Leaves often appear wilted during the day but regain their rigidity overnight.

At the beginning stages, plants with Fusarium wilt may also develop yellow foliage. However, the yellowing is often sporadic. For example, one side of the plant may turn yellow while the other remains green, or only leaf tips may turn yellow.

If you peel back the outer layer of the plant stem, you will notice the interior is red or brown. 


Fusarium wilt often enters gardens on infected transplants and spreads on equipment and tools. Therefore, purchase transplants from trusted sources and clean equipment and tools between each use.

Choose resistant cultivars if they’re available. For example, ‘Mountain Merit’ tomatoes are less likely to become impacted by Fusarium wilt than non-resistant varieties.


There is no cure for plants infected by Fusarium wilt. However, you can remove diseased plants to help prevent the infection of other plants. It is also notable that in acidic soil, increasing the soil pH to 7 can help to control or reduce the incidence of Fusarium in some plant species.

Downy Mildew

Close-up of plant leaves affected by Downy Mildew against a blurred green background. Leaves affected by Downy Mildew on plants display pale to yellowish-green areas with angular patterns, resembling patches or spots. The leaves are heart-shaped and have wavy edges with finely jagged edges.
Prevent it by controlling humidity, using resistant varieties, and applying fungicides if needed.

Downy mildew isn’t a true fungus but rather a water mold. However, growers often mistake it for a fungal disease. It can impact various plants, including ornamentals like snapdragons and stock, and vegetables like cucumbers and squash.


Downy mildew first appears as small, water-soaked lesions on the undersides of plant leaves. These spots eventually become present on the top of leaves as they enlarge and turn yellow or brown. Leaves eventually become covered in a fuzzy gray or brown coating.


Downy mildew is more likely to occur in humid and moist conditions. Therefore, choose drip irrigation rather than overhead watering to keep leaves dry. Using wider plant spacing and pruning compact plants will help increase airflow and limit humidity.

Choosing downy mildew-resistant varieties will also decrease the chances of infection. Growing in protected structures like high tunnels will help keep foliage dry and prevent disease.

Preventative applications of fungicides can also help stop downy mildew.


If you notice downy mildew on your plants, fungicides are the only way to save them. A copper fungicide on the entire plant will prevent infection but won’t cure infected tissue. Continue to reapply copper fungicide every week, ensuring you follow recommended application rates. Sulfur fungicides can also be effective, but copper is better.

Do not use both types of fungicide at the same time, as this can cause leaf tissue damage. Similarly, do not use either of these fungicides at the same time as using a neem oil or horticultural oil.

Powdery Mildew

Close-up of Coccinia grandis leaves affected by Powdery mildew on a blurred background. Coccinia grandis leaves are heart-shaped and bright green in color. They have a smooth and glossy texture with prominent veins running through the surface. The leaves are 3 to 5-lobed. Leaves affected by Powdery mildew display a characteristic powdery white to gray fungal growth on the upper surface of the leaves, resembling a fine dusting or coating.
Identify it by the powdery appearance on leaves, and prevent it by planting in full sun and maintaining good airflow.

Powdery mildew is the generic term for a group of fungal species, with each fungus impacting specific plant species. This disease can be challenging to prevent since it occurs in both wet and dry conditions.


As its common name suggests, powdery mildew makes plants appear dusted with flour or powdered sugar. This powdery appearance emerges as spots, which then cover entire leaves. Underneath the leaves, there may be greyish masses of sporulation for a few species of powdery mildew, but in most cases, it will be isolated to the upper surface.

If left untreated, infected leaves may become discolored and drop.


Unlike many fungal diseases, powdery mildew can occur in wet and dry conditions, so keeping foliage dry won’t prevent infection. Planting in full sun and maintaining good airflow can stave off powdery mildew.

However, planting resistant varieties is the best prevention strategy. Spraying plants with a sulfur fungicide can also prevent infection.


You can eliminate mild powdery mildew infections by spraying infected tissue with neem oil or other horticultural oils. However, avoid spraying oils when temperatures are above 90°F.

Septoria Leaf Spot

Close-up of tomato leaves affected by Septoria Leaf Spot in the garden. Tomato leaves display small, circular lesions with a dark brown to black center and a lighter, yellowish margin. Tomato leaves are dark green and pinnately compound, consisting of several leaflets. Each leaflet is lance-shaped with serrated margins.
Treat it by removing affected foliage and using organic fungicides like chlorothalonil or copper fungicides.

Septoria leaf spot infects the Solanaceae family’s tomatoes, eggplants, peppers, and other crops. This disease begins as seemingly harmless spots but can quickly defoliate plants.


The first sign of septoria leaf spot is small, round dots on lower leaves. These spots are brown or deep purple and may be surrounded by yellow tissue. If left untreated, entire leaves become discolored and eventually drop.


Although septoria leaf spot isn’t soil-borne, it can exist on infected plant tissue from one season to the next. When soil splashes onto lower leaves, plants may become infected. Therefore, mulching the ground with landscape fabric, straw, or wood chips can help prevent plant infection by preventing water from splashing up from the soil below.

Pruning off lower leaves and watering via drip irrigation can also help prevent infection. 


Remove and dispose of the foliage if you notice signs of septoria leaf spot on lower leaves. In some cases, this quick action prevents the spread of disease and maintains a healthy plant.

Spraying the organic fungicide chlorothalonil can help control infection and prevent spread. Copper fungicides can also help prevent the spread of the disease.


Close-up of Potato leaves affected by Phytophthora in a sunny garden. Leaves display dark, water-soaked lesions. The leaves are curled, withered, with dark brown rotting edges.
Phytophthora causes root and crown rot in herbaceous and woody plants, with symptoms like wilting and limited roots.

Phytophthora is a genus of water molds that cause root and crown rot. Various Phytophthora species infect herbaceous and woody plants.


Growers often notice above-ground symptoms like wilted and discolored leaves. Plants sometimes suddenly wilt during the first warm day since they can’t absorb the necessary water.

If you dig up a plant, you will see a limited root system; plants may have a few large but few feeder roots. The roots that do exist show discoloration and general decay. If you cut a root crosswise, you’ll notice the vascular tissue is red or brown.

Since other fungi can cause similar symptoms, looking at the environment can indicate what fungus is the culprit. Pythopthera only occurs in constantly wet or moist soils.


Pythopthera occurs when the soil remains moist for an extended period. Therefore, you can prevent Phytophthora by providing adequate draining and avoiding overwatering.  

Loosen outdoor soil with a digging fork before planting, and choose a well-draining potting mix for potted plants. Remember to allow soils to dry out a bit in between irrigation events.


If a plant is severely wilted and discolored when you discover Phytophthora, you can’t do much to save the plant. However, plants in the early stages of infection can recover if you decrease watering and apply a biological fungicide to the soil.

Sclerotinia Stem and Crown Rot

Close-up of Cauliflower plant suffering from Sclerotinia stem rot. Plant display white, fluffy, and cotton-like fungal mycelium on the stems and leaves, along with water-soaked lesions.
Identify it by white, fluffy growth and prevent it with humidity control and good airflow.

Also known as white mold, Sclerotinia stem and crown rot is a disease caused by the pathogens Sclerotinia sclerotiorum and Sclerotinia trifoliorum. It affects plants, including beans, sunflowers, canola, cabbage, and tomatoes. It is most likely to occur in cool, damp conditions.


An obvious sign of Sclerotinia is white, fluffy growth where the stem is infected. This growth is the mycelium of the fungus. Infected stems will eventually wilt and die back.

You may notice water-soaked lesions and subsequent white mold in crops such as cabbage and collards. Dark spots called sclerotia may also appear with the white mold.


Since Sceroltinia is most likely to occur in cool and damp conditions, limiting humidity and increasing airflow can help prevent infection. Clear weeds away from crops to allow for airflow and avoid overhead irrigation.

Removing crop debris in the fall can help prevent infection in the spring. Since the fungus can survive on weedy plants, you should remove any weeds.


While some fungicides can eliminate Sclerotinia, none of these products are for organic use. Therefore, prevention is often your best defense against this fungal disease.

Verticillium Wilt

Close-up of Tomato plants affected by Verticillium Wilt. The plant has wilted, rotted, browned leaves with dark spots. The stems are weak, soft, rotting, yellowish with brown spots.
Verticillium wilt damages the vascular system of various plants, causing wilting and yellowing.

Verticillium wilt enters a plant through the roots and damages the vascular system. It can impact various plants, including woody trees, shrubs, vegetables, and herbaceous flowers.


Sudden wilting of an entire plant or a portion of a plant is a common sign of Verticillium wilt. Plants may wilt during the day and recover at night. You may also notice leaves turning yellow or wrinkled.

Some plants develop dark streaks under their bark or outer stem layer. You can peel back the bark or take a cross-cut of a stem to check for this streaking.


Choose resistant cultivars when they’re available. These varieties will be less likely to become infected by Verticillium wilt.

Removing infected tissue and practicing crop rotation also helps prevent the onset of Verticillium wilt. Keeping your garden weed-free is another preventative measure.


You cannot cure infected plants. However, encouraging new growth helps plants remain healthy for an extended period. Water well and provide plants with a boost of nitrogen-rich fertilizer.

Leaf Rust

Close-up of fruit tree leaves affected by the fungal disease Leaf Rust. Leaves display small, round, orange to reddish-brown pustules and rust-colored lesions on the upper and lower surfaces. The leaves are medium in size, heart-shaped, glossy green.
Leaf rusts cause orange to red-brown spots on foliage, which can spread to turn entire leaves rust-colored.

Leaf rust is a group of fungal diseases that cause rust-colored patches on foliage.


All types of leaf rusts cause foliage to develop orange to red-brown spots. These spots can spread and cause entire leaves to appear rust-colored.


The best way to prevent leaf rust is to plant resistant varieties. Other preventative actions include avoiding overhead irrigations, removing plant debris, and spacing plants for good airflow.


It’s important to note that plants, including apples, hawthorn, and roses, can tolerate leaf rust without many adverse effects. As long as the plants aren’t dropping leaves, they are likely going to survive. If you start to see significant leaf drop, this may be time to look for additional problems beyond the rust.

Spraying plants with some commercial fungicides helps prevent and treat infection in some crops, but these fungicides aren’t organically approved. Instead, spray neem oil or sulfur to prevent the spread of infection, although these methods will not treat the rust. Carefully pruning off damaged tissue and removing it from the garden can prevent some spread via sporulation.


Close-up of tomato leaves infected with Alternaria. Leaves exhibit dark, concentric, target-like lesions with a bull's-eye pattern on their leaves, which are brown to black in the center and surrounded by a yellow and brown ring.
Prevent with resistant varieties, drip irrigation, and proper spacing.

Alternaria is a genus of fungal species that attack plants, including asters, calendula, and zucchini. The genus of Alternaria that infects tomatoes (Alternaria linariae, previously called Alternaria solani) is often called early blight.


Alternaria creates dark lesions on plant leaves. These lesions often exhibit concentric circles of dark brown and light brown colors. The areas surrounding the lesions often turn yellow. Eventually, leaves will turn brown and fall off.


If possible, choose varieties that are resistant to Alternaria.

Avoid overhead irrigation and opt for drip irrigation. Maintain proper plant spacing to encourage good airflow.


Spray infected plants with a copper fungicide. 


Close-up of leaves Grape leaves affected by Anthracnose. Leaves exhibit small, round to irregularly shaped lesions that are initially water-soaked and turn brown or black. Grape leaves are large, palmately lobed, and dark green in color. They have serrated edges and are known for their distinctive shape.
Prevent with resistant varieties, regular harvesting, proper spacing, and mulching.

Anthracnose is a group of fungal diseases that infect plants, including trees, vegetables, flowers, and turf.


Anthracnose symptoms vary depending on the infected plant and weather conditions.

The disease infects young leaves and twigs on trees and shrubs, leading to dark spots, larger lesions, or leaf drop. Some trees experience curled leaves.

Anthracnose causes dark, water-soaked lesions on the fruits of vegetable plants, including squash, beans, peppers, and tomatoes. It can also lead to small, dark spots on plant foliage.


Choose anthracnose-resistant varieties when possible.

Since anthracnose is more likely to infect ripe fruits and vegetables, harvest regularly to avoid overripe produce.

Avoid overhead irrigation and space plants to allow for good airflow. Mulching around low-growing plants like tomatoes and squash can help prevent infection.


Once plants are infected with anthracnose, you cannot treat the disease. However, you can prune off infected portions of trees and shrubs and spray uninfected growth with a fungicide to prevent further infection.

Grey Mold

Close-up of Strawberry fruits affected by Botrytis on a blurred green background. The berries have gray to brownish, fuzzy fungal growth on the surface. The infected areas appear water-soaked, soft, and mushy.
Identify it through brown spots and fuzzy gray growth.

Also known by its genus name Botrytis, gray mold impacts flowering and fruiting plants, including strawberries, grapes, peonies, dahlias, and larkspur. Spores can also lay dormant and infect fruits after you place them in cold storage. 


The first signs of gray mold are small, brown, water-soaked spots on foliage and stems, or a fuzzy, gray material eventually replaces these spots. The fuzz can cover entire fruits and stems.


Since gray mold is more likely to occur in moist conditions, aim to keep plants dry. Avoid overhead watering and prune to allow for good airflow.

Grey mold attacks weak parts of the plant, like overripe fruit and old, discolored leaves. Therefore, regular harvesting and pruning limits gray mold. Removing fallen foliage and flowers from the ground also limits the disease.


Once fruit, flowers, or foliage is infected with gray mold, it won’t recover. However, you can protect infected parts of the plant from infection.

Remove infected flowers and foliage to help stop the spread of gray mold to uninfected plant parts. Spraying plants with a biological fungicide like Regalia will also help limit infection.

Sooty Mold

Close-up of tree leaves affected by Sooty Mold. Leaves develop a black, powdery, or flaky fungal coating on their surface. This mold covers the leaves in a layer that can obscure the green color of the foliage underneath.
Sooty mold results from fungal colonization of the honeydew secreted by sap-sucking insects.

Sooty mold often occurs when sap-sucking insects secrete a sugary honeydew. The gray mold impacts plants and can discolor cars, sidewalks, and other items. Numerous fungi genres cause sooty mold.


Plants infected with sooty mold look like they’ve been covered with gray ash. While sooty mold doesn’t directly harm plants, it limits photosynthesis. Therefore, plants may become stunted if you don’t address the sooty mold.


Since sooty mold only occurs when honeydew is present, keeping plants free of sap-sucking pests like aphids, mealybugs, and whiteflies will prevent this fungal disease. You can treat these pests by spraying them with neem oil or insecticidal soap.


The first step of treating sooty mold is treating the pests secreting the honeydew. Once honeydew is off the plant, the fungus will fade.

Spraying plants with neem oil or insecticidal soap can also help wash off the sooty mold and help plants recover.

Rhizoctonia Rot

Close-up of a gardener's gloved hand holding Soybean roots affected by Rhizoctonia Rot against a background of growing Soybean plants. Soybean roots exhibit dark brown to reddish-brown lesions or cankers on the root surface.
Rhizoctonia root rot leads to reddish-brown spots on roots and stems, causing stunted, wilted plants.

The fungus Rhizoctonia solani commonly causes seed decay and root rot. It impacts a wide variety of plants at various life stages.


Rhizoctonia root rot causes plants’ roots to develop reddish-brown spots on their roots and portions of stems near the soil. The stems eventually become shrunken, with a girdled appearance. Above ground, plants often appear stunted, discolored, or wilted.

The fungi can also cause small seedlings to die just before or after emergence. This phenomenon is commonly known as “damping off.” While other fungi can cause damping off, Rhizoctonia prevails in dry and warm soil.


Rhizoctonia often enters plants on open wounds, so handle plants with care. Avoid pruning near the soil surface.

Rhizoctonia is soil-borne, so avoid reusing infected potting mix. Thoroughly cleaning seed trays also helps prevent the spread of disease.

Additionally, treating your soil with a biological fungicide can help protect plant roots against Rhizoctonia infection. 


Once plants are infected with Rhizoctonia, treating the soil with biofungicides will encourage plants to recover. However, this disease will often kill infected plants.

While some fungicides will effectively eliminate Rhizoctonia, they are not organically approved. 

Final Thoughts

Plants of all kinds are susceptible to fungal diseases. And while you may feel defeated watching your plants succumb to these diseases, knowledge can help you keep your plants healthy! Knowing the symptoms of each disease allows you to identify the problem and prevent further infection.

Remember that moisture and airflow impact the development of many fungal diseases, so pay close attention to how you water and how far you space plants. And if you notice a disease one year, aim to plant resistant varieties in the future.

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