How to Identify, Treat and Prevent Septoria Leaf Spot in Tomatoes

You might be wondering what those spots are on your tomato leaves. Join gardening expert Jenna Rich as she goes over how to spot Septoria Leaf Spot on tomatoes and what you can do to prevent it.


Hooray, it’s finally tomato season! Unfortunately, tomato pathogens are also in season and ready to attack weak plants. Septoria leaf spot is one of the most common tomato diseases. Here is how to identify, treat, and avoid it in the future.

What is Septoria Leaf Spot?

Close-up of tomato leaves affected by Septoria Leaf Spot. The plant has upright hairy stems with compound leaves. The leaves consist of bright green oval leaflets with slightly serrated edges. The leaves are covered with small round yellowish-brown spots with dark concentric rings or edges.
This global fungal disease devastates tomato plants, affecting all growth stages.

Septoria leaf spot, also called Septoria blight, is a fungal disease that occurs worldwide, most often in tomato plots. It has been known to take out 100% of affected areas during a nasty outbreak. Dangerously, it can affect tomatoes at any growth stage.

What Causes Septoria Leaf Spot?

The fungus Septoria lycopersici is the perpetrator and spreader of this disease. It can be highly detrimental to gardens and farms or any other location where tomatoes are grown. The fungus begins by attacking older leaves, so growers usually notice spots on the lower parts of the plant first.

Conditions and Crops

Septoria lycopersici thrives in extended wet, warm, and humid periods. The leaf spots often show up after heavy rain when there is still high humidity.

This is considered a tomato disease but has been known to show up in other Solanaceous plants such as eggplant, potatoes, and petunias.

Identifying Septoria Leaf Spot in Tomatoes

There are many types of leaf spot disease, including Cercospora leaf spot and Alternaria leaf spot. Here’s how to differentiate Septoria from the others so you can properly deal with it.


Close-up of a fox tomato infested with Septoria Leaf Spot. The leaf is oval, with deeply serrated margins. It is pale green in color with yellowish spots. Many irregular small brown-black spots are on the surface of the leaf.
It starts as small spots on tomato leaves that can merge, and may cause leaf drop and fruit sunscald.

The first sign of this disease is small, perfectly round spots on the underside of tomato leaves. These spots will have dark brown margins and may be tan or greyish in color, sometimes with small, black fruiting bodies on the underside of the leaf just below the spots.

As the disease progresses, the spots may become larger and appear to merge, but you can generally still see some dark brown margins in the spots. Symptoms typically only appear on the leaves of tomatoes, but spots can also occur on stems and petioles.

If your plants have a particularly bad case of this fungal disease and spots are numerous, the leaves will likely turn yellow and fall off, affecting the oldest leaves first.

It can quickly move up the plant, especially if conditions are right. Due to the loss in leaf coverage, this can lead to sunscald of unprotected fruit.

Fruit is rarely affected directly by the disease.

Septoria Leaf Spot vs. Early Blight

Combined two images with different tomato leaf diseases: Septoria Leaf Spot vs Early Blight. Leaves infected with Septoria Leaf Spot have small, irregular, dark brown spots. A leaf infected with Early Blight disease has one large brown spot with a yellowish halo.
Early blight has irregular circles with brown halos, whereas Septoria leaf spot has small, round spots.

These two diseases can sometimes be confused due to the presence of spots and yellowing leaves. However, they have differences you should look for to make a correct diagnosis.

Early blight has irregularly shaped circles, typically brown in color. Larger blight spots can sometimes have concentric rings inside larger spots with yellowing of the leaf tissues around the spot. In contrast, Septoria Leaf Spot features petite, very round spots with a light center that sometimes merge together as the disease progresses.

The other tell-tale sign of Septoria is the presence of tiny bumps inside the tan or grey centers of the spots, often on the underside of leaves. These are called pycnidia and are the fruiting bodies of the fungus.

How to Dispose of Infected Plants

Close-up of the hands of a gardener in black gloves with scissors cutting off the affected leaves of a tomato, in the garden. The tomato plant has pale green stems covered with small hairs, compound dark green leaves. The leaves consist of oval leaflets with serrated edges.
Identify and remove infected leaves, clean tools, and change clothes to prevent spread.

If you notice symptoms of this disease and have positively identified it, immediately begin to remove infected leaves and remove all debris from your garden.

Use clean tools and gloves, disinfect your tools between tasks, and change your clothes before moving to an uninfected area of your garden. Try doing this task when the leaves are dry as the fungal spores can easily spread via water.

Pro tip: You can remove up to ⅓ of a plant’s leaves without damaging its growth. Just keep in mind you may open up some of your fruit to sunscald if you remove a leaf canopy above a ripening cluster.

If the infection is severe, remove the entire plant and move it to your burn pile. Do not compost infected material as the spores can live on in the compost.

How to Prevent

Tomato diseases tend to spread quickly, so prevention is key. Here’s how to keep this nasty pathogen out of your garden.

Remove Plant Debris in the Fall

Close-up of a gardener in white gloves cleaning up the debris of tomato plants in the garden. The tomato plant has pale green stems, complex dark green leaves. The leaves consist of oval leaflets with serrated edges. Leaves and stems are mostly dry, brown in color. Tomato fruits are small, oval-shaped, hard, green in color with brown rotten spots. The gardener is dressed in jeans, a blue T-shirt and a straw hat.
To prevent reinfection, remove all tomato debris from the garden area, including clippings, suckers, and fallen fruits.

Septoria lycopersici will overwinter on any tomato debris, so all parts must be fully removed from your gardening area. This is a great fall task when you are cleaning up your beds at the end of the season. Plant and leaf debris left behind to overwinter in the soil is the main source of the inoculum of this fungal disease.

This includes clippings, suckers, leaves, fallen fruits, and any other plant parts, so be sure to take all uninfected material to the compost pile at the end of the season to prevent its development or spread. If you know the disease is present, remove the infected material from your property completely or burn it.

Practice Crop Rotation

Planting tomato seedlings in the garden. Close-up of a gardener's hands in white gloves planting young tomato seedlings in a hole in the soil. The seedlings have upright stems of a pale green color covered with fine white hairs. The leaves are compound, composed of oval leaflets with serrated edges.
Crop rotation prevents recurring diseases and pests by shifting the location of plants so they don’t stay in the same place.

Crop rotation is a good way to prevent the same diseases and pests from attacking your garden plot year after year. If possible, rotate tomato beds with non-Solanaceous crops.

This means you should avoid planting related nightshade crops (eggplants, peppers, petunias, etc.) in the same bed several seasons in a row. If possible, wait at least two years before planting tomatoes there again.

Invert the Soil

Close-up of a gardener with a shovel digging up the soil, in a sunny garden. The gardener is dressed in dark brown pants, brown sneakers, and a brown long-sleeved shirt. A shovel with a long wooden handle is completely filled with soil.
Deep soil inversion can reduce infection risk.

If crop rotation is not possible or your plot is very small, a very deep inversion of the soil may help reduce the chances of an infection. Use a broadfork to dig into the bed and flip the soil upward.

This technique can bury any fungal spores that are on the soil’s surface, preventing them from being splashed up onto tomatoes. It also loosens up compacted soil, aerating it and making it easier for roots to penetrate.

Grow Grafted Tomatoes

Close-up of a seedling of a grafted tomato plant in a garden. The seedling has an upright pale green stem with large compound leaves that consist of oval green leaflets with serrated edges. A drip irrigation system has been laid on the soil.
Grafted tomatoes may show delayed susceptibility to some diseases.

Some growers claim their grafted tomatoes were slower to succumb to disease, but this delays the inevitable. Grafting is when an heirloom or a coveted variety of tomatoes is spliced onto the rootstock of a resistant tomato. While the rootstock does convey some resistance to common garden diseases, that doesn’t mean it’s fully immune to them; a bad infection can still occur.

If you are familiar with grafting or can buy grafted plants from a trusted source (like a local organic farmer), I recommend giving it a shot. This is doubly true if you grow in soil that may have fungal spores present. Grafting onto a resistant rootstock might get you a few more weeks of harvest time.

The downside to this plan is that no rootstock cultivars are known to be resistant to Septoria fungi. This does not mean you shouldn’t look for resistant cultivars, as new tomato varieties come out every year, but you may only be able to find varieties resistant to other diseases.

Avoid Overhead Watering

Close-up of watering a tomato seedling in the garden, on a blurred green background. The seedling consists of an upright stem covered with fine, fine white hairs. The plant produces compound leaves from green oval leaflets with serrated edges. Close-up of a hose with a black and yellow spray nozzle. Water is directed to the base of the plant.
Water plants at the base to prevent spore spread, avoiding wet foliage and splash-up.

Wet foliage and droplets on leaves can assist in the spread of many harmful spores. The moist surface catches and anchors any wind-borne spores, allowing them to take hold on a leaf’s surface. It’s best to water at the base of your plants to avoid any water splash on the foliage.

Water early in the day so plants can drink up and any lingering droplets have a chance to dry quickly once the sun comes out.

Create a Pest Management Plan

Close-up of spraying a tomato plant from a red and black sprayer. The plant produces complex light green leaves and large, round fruits that are green and yellowish in color. The fruits are firm, juicy, with a shiny thin skin.
Prevent disease spread by controlling pests that unintentionally carry spores on their bodies.

Pests unknowingly spread diseases of all kinds, including this one. As they hop or fly around your garden, spores that have caught on hairs on their bodies are transported from crop to crop. Keep pests at bay to help avoid this method of spreading disease.

Mulch Your Plants

Mulching a tomato plant in the garden. Close-up of a gardener's hands in gray gloves adding a layer of straw mulch to a tomato bed. The plant produces upright, slightly hairy stems with compound, light green leaves. The leaves consist of oval leaflets with serrated edges.
To prevent disease spread, mulch with well-composted materials to reduce water splashing and weed contamination.

This disease often spreads by water splash and travels with plant debris or soil. Mulching your pathways and plant beds can help minimize any water splashing soil (and hidden spores) up onto the leaves, which can suppress the spread of disease. Be sure the mulch is well-composted. You can also try using landscape fabric or black compostable plastic mulch.

Remember, nightshade and horsenettle weeds can become infected with this pathogen, so covering paths and surrounding areas should help keep weed pressure down.

Keep a Tidy Garden

Top view, close-up of starter seed trays filled with soil. Trays are plastic, black, with square deep cells filled with soil mixture.
Prevent fungal contamination by thoroughly cleaning seed-starting supplies each season.

If you are starting seeds each year or growing crops in a greenhouse, clean all of your seed-starting supplies or greenhouse spaces each season to ensure there are no lingering spores present. This includes cell trays, 1020 trays, work benches, reusable tags, etc. A diluted bleach spray is the best way to sanitize.

Septoria lycopersici can also travel on clothing, shoes, or other gardening supplies, so take care when walking through tomato fields or high tunnel growing areas.

Prune for Airflow

Pruning tomatoes in the garden. Close-up of black pruners with green handles of a cutting plant. The plant has thin pale green stems covered with fine hairs. The plant has complex pinnate leaves, which consist of oval green leaflets with serrated edges. The fruits are small, rounded, with a shiny smooth green skin.
Allow plants space to breathe, ensure good airflow, and prune leaves regularly to prevent disease spread.

The more space your plants have to spread out and breathe, the better. Good airflow also helps your plants dry out daily. Examine your plants every week or two with a clean pair of snips in hand, and prune unnecessary or damaged leaves from the bottom.

YouTube video
Properly pruning your tomatoes can help limit disease.

This is a great habit to avoid spreading disease, as spores can jump from plant to plant if leaves are touching. If you do discover disease symptoms, sanitize your tools between plants.

How to Treat

Spraying tomato plants with fungicides to prevent the spread of fungal diseases. Close-up of a gardener in protective white gloves with a sprayer in his right hand, spraying a plant. Sprayer of gentle blue color with a white nozzle. The tomato plant has lush, complex green leaves. The leaves consist of oval leaflets with serrated edges. The plant produces large and small round fruits. They are juicy, firm, with a shiny thin skin of red color.
Early treatment with appropriate fungicides is crucial for preventing and managing this fungal disease.

Prevention is really key, especially with this disease. If your garden is prone to this disease or you suspect it might attack, treat it immediately before symptoms are rampant. You have a few options:


Fungicides containing sulfur or copper are best used very early in the disease cycle. Ensure the label specifies that the application is appropriate for vegetables; as always, read the full label before use. You may need to delay harvest after application to ensure the fungicide has broken down enough and fruits can safely be consumed. Many growers are applying these fungicides in early to mid-July when conditions tend to be best.

Foliar Treatments

Foliar treatments with the active ingredient potassium bicarbonate have been shown to treat and prevent future infections of many fungal diseases, including some leaf spots, downy mildew, powdery mildew, anthracnose, and rust. Manufacturers of these treatments claim they give two weeks of protection and can be used in conjunction with other treatments and that it destabilizes fungi at a cell level while changing the pH to prevent future breakouts.

Read Labels and Use Caution

Organic and chemical sprays can be sprayed every 7-10 days between flowering and fruit-setting growth stages. Consult with an expert and read all the labels before starting any treatment. Follow any delayed harvest instructions per the labels to ensure safe consumption; this step is important for your own health.

Chemical treatments, including chlorothalonil and mancozeb, are safe for homeowner use.

Frequently Asked Questions

Can Septoria lycopersici survive in soil over the winter or in old plant matter?

Yes, Septoria lycopersici, the fungus that causes Septoria leaf spot, can and does survive in soil over winter months. If there is infected plant debris present in the soil, there is also pycnidia, those fruiting bodies.

The pycnidia begin to create spores when conditions are just right, which can then be spread to healthy plants by way of wind, water splash, hands and clothes of workers, equipment, during cultivation, and even by pests. The spores then begin to germinate on healthy plants, infecting the tissues. Symptoms will likely show up in about 5 days. This cycle will continue as spores spread and new infections begin.

Are there Septoria Leaf Spot-resistant cultivars on the market?

Unfortunately at this time, there are no known Septoria leaf spot-resistant tomato cultivars. However, there are some cultivars that are resistant to other tomato diseases, and these can be beneficial.

Where can I get more information on Septoria Leaf Spot?

Contacting your local cooperative extension office is a great starting point. Most extension offices have a diagnostic lab that will test samples for a small fee. Just check their website and follow the mail-in instructions. Many state extension offices also offer fungicide application and pesticide safety training courses and some states even offer certifications.

You can also find a local gardening club, find a master gardener club, or join a Facebook gardening group and ask fellow members for advice. Gardeners love to share tips and advice!

Final Thoughts

The positive identification of common garden diseases is key to prevention and proper treatment. Knowledge is power! Have a plan of action in mind if the need arises, be confident in your actions, and know that your tomato plants are in good hands.

Tomato plant with yellow flowers blooming in the garden

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