Black Dots on Tomato Leaves: 9 Causes and How to Tell Them

Black dots on tomato leaves point first to four diseases: bacterial speck, bacterial spot, Septoria leaf spot or early blight. Size, shape and the weather tell them apart. The UMN Extension tomato diagnosis guide describes speck spots of about 2 mm with a yellow halo, Septoria spots under 1/8 inch with tiny black dots in a tan center, and dark, irregular early blight spots with yellow tissue around them; UC IPM adds that early blight spots often show target-like rings.

Insects can leave dark marks too. Thrips leave black flecks of excrement, spider mites leave pale stippling with dark mites underneath, and whiteflies and aphids leave honeydew that grows black sooty mold. This guide gives a side-by-side comparison table, spot-size and weather charts, a five-step field check, and a copper calculator so you can keep sprays within the label limit.

What causes black dots on tomato leaves?

Here are the nine causes covered in this guide, with the one clue that points to each. The first four are the common diseases. The last five are look-alikes that need a different fix.

1. Bacterial speck (Pseudomonas syringae pv. tomato). Look for: very small, round black spots with a yellow ring, in cool, wet spring weather.
2. Bacterial spot (Xanthomonas species). Look for: small black spots that are angular, greasy or torn in the middle, in warm, wet weather.
3. Septoria leaf spot (Septoria lycopersici). Look for: many small round spots with a dark edge, a tan or gray center and pin-point black dots inside.
4. Early blight (Alternaria linariae, formerly A. solani). Look for: larger brown-black spots with rings like a target, low on the plant first.
5. Late blight (Phytophthora infestans). Look for: irregular water-soaked patches that turn olive, then brown, and spread fast.
6. Thrips. Look for: silvery or pale scars dotted with shiny black specks of excrement (frass).
7. Spider mites. Look for: fine pale stippling on top of the leaf and tiny moving dots and webbing underneath.
8. Sooty mold from whiteflies or aphids. Look for: a black film that sits on a sticky surface and can be washed off.
9. Flea beetles. Look for: tiny round pits and holes and small black beetles that jump.

Two other things can cause dark marks: copper or other spray injury, and old leaves that are simply dying from the bottom up. The sections below cover each cause, then the treatment options.

How to tell black spots on tomato leaves apart

Use this table with a hand lens. Check the top and the underside of several leaves from the lower, middle and upper plant. One leaf can mislead you, and two diseases can be present at once.

Size is the quickest first clue. In the extension descriptions we used, speck and Septoria spots stay very small, bacterial spot can grow to about 7.5 mm, and early blight spots reach 6-12 mm. The chart below shows the largest typical leaf-spot size for each disease.

Size alone is not enough, though. Bacterial speck and bacterial spot look alike on leaves. UConn Extension says spot lesions are round to angular while speck lesions are only round, and that fruit spots are a better guide: bacterial spot makes larger, scabby fruit spots. For a firm answer, a lab can check whether bacteria ooze from cut tissue in a drop of water.

Chart

How big the leaf spots get

Largest typical leaf-spot diameter in extension descriptions, mm

The four common diseases behind black spots

1. Bacterial speck

UConn Extension calls bacterial speck the most common bacterial disease of tomato. Leaf spots are round, dark brown to black and may get a pale ring as they age. The spot goes all the way through the leaf and is easiest to see from below. Nearby spots can merge into dead patches, and on young leaves the tissue between spots may tear as the leaf grows.

On fruit, speck makes raised black flecks smaller than 1/16 inch. UC IPM says the bacteria survive in soil, in plant debris and on seed, and spread by splashing rain or sprinkler water. Hot weather stops the disease. In California, UC IPM notes that many varieties resist race 0 of the pathogen but none currently resist race 1, which is the main race there.

2. Bacterial spot

Bacterial spot is caused by several Xanthomonas species, mainly X. perforans, according to Clemson Extension. It also infects pepper. Leaf spots are small, water-soaked at first, then black. Their centers dry out and often tear, leaving a ragged hole. In very wet weather the leaves look blighted rather than spotted.

The bacteria are carried in and on seed and on transplants, and they survive in crop debris, on volunteer tomatoes and on weeds such as nightshade and groundcherry (UC IPM). Symptoms develop fast at 68°F and above, while nights at 61°F or below hold the disease back. Penn State Extension notes that young bacterial spot lesions can be hard to tell from early blight.

3. Septoria leaf spot

Septoria leaf spot is the cause when you see many small round spots with a dark edge and a pale center. The tiny black dots inside are the fungus’s spore-producing bodies. The UMN guide says these dots appear about eight days after the spot itself. The fungus does not infect fruit, but heavy leaf loss exposes fruit to sunscald and reduces fruit size and quality, according to Clemson.

Infection usually starts on the lowest leaves after the plants begin to set fruit. Clemson Extension says the fungus is most active at 68 to 77°F with high humidity and wet leaves. It is not soil-borne, but it overwinters on crop residue and on weeds related to tomato.

4. Early blight (Alternaria)

Early blight starts as small brown lesions on the oldest leaves. They grow into spots of 6-12 mm, often with rings like a target (UC IPM), and the tissue around them may turn yellow (Clemson). Penn State Extension says damage is usually limited to the lower third of the plant, but warm, humid weather can kill much of the foliage. Stem lesions near the soil line can girdle young plants, a symptom called collar rot.

The fungus survives on infected debris, on seed, on volunteer tomatoes and on related plants such as potato, eggplant and black nightshade. Spores spread by wind and splashing water and need a wet leaf to infect. For a full treatment comparison, see our guide to organic and chemical early blight control.

▶ Bacterial canker of tomato, another bacterial disease: how to spot it and manage it with clean seed and sanitation. · 15:25

Weather clues: which disease fits this week

Each disease has its own comfort zone. If your plants got black spots after a cool, wet spring week, speck is more likely than bacterial spot. If the spots came after a run of warm, stormy nights, bacterial spot moves up the list. Septoria and early blight both need wet leaves, but they also need warmth. The chart shows the temperature ranges the extension services give.

Use the ranges as a guide, not a rule. Wet leaves matter as much as temperature. Long dew periods, rain splash and overhead sprinklers all spread spores and bacteria. Clemson Extension says most bacterial spot outbreaks can be traced back to heavy rainstorms in the area.

Chart

Temperatures that favor each disease

°F, ranges given by extension services (wet leaves are needed as well)

Look-alikes: late blight and spray injury

Late blight is the look-alike that needs the fastest response. The UMN guide describes irregular, water-soaked patches that turn olive and then brown. In wet weather a white growth covers the infected tissue, and the disease spreads very fast in cool, wet weather. If you suspect late blight, contact your local extension office right away, because it spreads quickly.

Spray injury can also leave dark specks or burned edges. EPA’s 2009 copper review records a case of tomato damage in Washington State after copper was applied as the label directed. If dark specks appear soon after a spray and do not keep spreading, ask your extension office whether spray injury is the cause.

▶ How spray and chemical injury (phytotoxicity) shows on crop leaves, and how to avoid it. · 19:28

Insects that leave black dots on tomato plant leaves

Thrips frass

Thrips are tiny, slender insects less than 1/20 inch long. UC IPM says they feed by piercing the leaf surface and sucking out cell contents. This leaves stippling, pale flecks or a silvery sheen, usually with black, varnish-like flecks of frass. If the dark marks sit on top of silvery scars and do not have a halo, thrips are the likely cause. Look for the insects in flowers and on leaf undersides before you treat.

Spider mite stippling

Spider mites look like tiny moving dots to the naked eye. UC IPM says damage first shows as a stippling of light dots on the leaves, which may turn bronze, yellow and then drop. Webbing on the underside is a strong clue. Damage is worst in hot, dusty conditions and on water-stressed plants. To check, shake a leaf over white paper and watch for moving specks.

Sooty mold from whiteflies and aphids

Whiteflies and aphids excrete sticky honeydew. Black sooty mold then grows on the honeydew. UC IPM says sooty mold does not infect the plant, but a heavy coat blocks light and can stunt growth. It can be washed off with water or mild soap and water. The real fix is to reduce the insects that make the honeydew.

Flea beetles and other small black bugs

Flea beetles are about 1/16 inch long, black, and jump when disturbed. The UMN guide says they chew small pits and holes, mostly in spring. These are holes, not spots, so they are easy to tell from disease once you look closely. For aphids and other dark insects, see our guide to small black bugs on plants.

A five-step field check before you spray

1. Look at where the spots are. Spots that start low and move up point to Septoria or early blight. Spots across the whole plant after a storm point to bacteria. Pale stippling with dark specks points to insects.
2. Use a hand lens. Tiny black dots in a pale center mean Septoria. Rings like a target mean early blight. Moving dots or webbing mean mites.
3. Check the fruit. Raised black flecks smaller than 1/16 inch fit speck; larger, scabby spots fit bacterial spot. Septoria never spots the fruit.
4. Wash the spot. A black film on a sticky surface that washes off is sooty mold, not a leaf disease.
5. Send a sample when unsure. Bacterial diseases, late blight and new outbreaks are worth a lab check. Your state or provincial extension office or plant disease clinic can confirm the cause.

Getting the cause right matters because the fix differs. Many fungicides for Septoria and early blight are not meant for bacteria; the UF/IFAS Florida tomato guide notes that mancozeb helps against bacterial spot only when tank-mixed with copper. Copper does not control insects or mites.

What to do about black spots on tomato leaves

Treatment starts with steps that work against every cause: clean fields, dry leaves and resistant varieties. Sprays come second, and the right spray depends on the cause you found.

Clean up and change how you water

Start with the steps every extension source agrees on. Remove infected lower leaves, keep debris out of the field and control nightshade, groundcherry and volunteer tomatoes. Water at the base with drip lines or furrow irrigation rather than sprinklers, and water early in the day so leaves dry before night. Our guide to furrow irrigation covers one low-cost option.

• Rotation: Clemson suggests a 3-year rotation for Septoria. Cornell suggests more than 3 years out of tomato and pepper for bacterial diseases. UConn suggests at least one year for speck and 2-3 years for bacterial spot.
• Clean seed and transplants: use certified seed, inspect transplants and destroy any with symptoms. Hot-water seed treatment can help against bacteria.
• Do not work wet plants: tying and pruning wet plants spreads bacteria.
• Stakes and mulch: use new stakes or clean old ones, and mulch to cut soil splash.
• Prune with care: Penn State suggests removing leaves within 12 inches of the ground at the first sign of early blight, but no more than 20% of the leaf mass.

Choose resistant or tolerant varieties

Resistance is the cheapest long-term fix. Cornell’s breeding program lists fresh-market hybrids with resistance to late blight and Septoria plus strong early blight tolerance, including Iron Lady, Stellar, BrandyWise and Summer Sweetheart. Its Plum Perfect hybrid also carries the Pto gene for bacterial speck resistance. Clemson’s tomato fact sheet lists more varieties with early blight resistance, such as Mountain Merit and Defiant PhR (both rated moderate).

Resistance is not immunity. Cornell notes that its Septoria resistance slows lesion growth but does not stop the first lesions from forming. Resistance to one speck race may not cover another, as the California race 1 example shows. Check seed catalogs and your local extension variety trials.

Copper sprays for bacterial speck and spot

Copper is the main spray for bacterial speck and bacterial spot, but it only gives partial control. UC IPM calls copper strictly a protectant: it must be on the leaf before an infection period, so timing before rain matters. It suggests repeat sprays every 10 to 14 days while conditions favor disease.

Bacteria can become resistant to copper. UC IPM says copper resistance is common in speck. Cornell says few copper-resistant isolates have been found in New York so far, but resistance is a major problem in the southern US. Adding mancozeb to copper improves its effect against bacteria, according to UC IPM and the UF/IFAS Florida tomato production guide.

A Cornell trial in Portland, New York, shows the size of the effect. In 2018, copper alone was not significantly different from untreated plants by the end of the season. Copper plus the Bacillus product Serifel cut the leaf area with speck by 35.5% on 27 September (33.3% vs 51.7% of leaf area) and by 23.5% on 3 October (48.9% vs 63.9%), relative to untreated plants. Serifel is not labelled for bacterial speck, and this is one site and one season, so treat it as an example, not a forecast. Cornell research suggests that Double Nickel or LifeGard can replace some copper sprays (the Double Nickel label says to tank-mix or rotate it with copper).

Chart

Bacterial speck through one season, by spray program

% of leaf area with symptoms, Portland, New York, 2018 (one trial site)

Copper limits per season

Labels and regulators cap how much copper you can apply. In its 2009 review, EPA set fresh-market tomato limits of 1.6 lb of metallic copper per acre per spray, 8.0 lb per acre per year and at least 3 days between sprays. Processing tomatoes had a lower per-spray limit (0.53 lb) but a higher yearly cap (17.4 lb). In the EU, copper use is capped at 28 kg per hectare over 7 years, an average of 4 kg per hectare per year, and many member states set 4 kg per hectare per year as the maximum, according to the EU Copper Task Force.

Chart

Yearly copper limits for tomato

lb of metallic copper per acre per year; EU figure is the 7-year average

The label states the product rate, not the metallic copper. To convert, multiply the product rate by the share of metallic copper on the label. The calculator below does this for your own program. Always check the label on the product you use: the label is the law, and your state, province or country may set stricter limits.

Try the numbers for your own farm below.

Labelled fungicides for Septoria and early blight

For fungal leaf spots, protectant fungicides work best when started early. Clemson Extension rates chlorothalonil as very good for Septoria and mancozeb as very good for early blight, with copper as good for both. For early blight in California, UC IPM lists chlorothalonil, mancozeb, fixed copper and a Bacillus subtilis biofungicide. Rotate products by FRAC group as the label and local guide direct, and never exceed label rates or the number of sprays allowed.

A weather model can space sprays. The TOMCAST model scores each day for leaf-wetness hours and temperature. In UConn Extension’s summary, the first spray goes on at 25 disease severity values (DSVs) after transplanting, then every 15 to 20 DSVs depending on the product. UConn warns that TOMCAST spray intervals are too long for copper, so do not use it where bacterial diseases are present.

Treating thrips, mites and honeydew insects

For thrips, mites and honeydew insects, monitor before you treat and protect natural enemies. UC IPM warns that broad-spectrum insecticides often cause spider mite outbreaks. UC IPM lists sprays of water, insecticidal oils or insecticidal soaps as options for mites, and soaps or oils for whiteflies. Keep plants well watered, because water-stressed plants suffer most from mites.

Pesticide rules differ by country, state and crop. Always read and follow the product label, check local rules (EPA and your state in the US, PMRA in Canada, HSE in Great Britain, APVMA in Australia) and ask your extension office or a licensed adviser before you spray.

Where satellite monitoring fits

A satellite cannot see a 2 mm leaf spot. What it can show is a block of a field whose plant cover is weaker than the rest, so you know where to walk first. The Farmonaut Satellite + AI Farm Monitoring System maps vegetation indexes for each field you draw, which helps on larger tomato plantings where scouting every row each week is hard. The leaf check, the hand lens and the lab are still how you name the cause. For more on field tools, see our list of precision agriculture tools.

Related pages on our site: agro admin app for large farms, fleet management, carbon footprinting, crop loan and insurance checks, product traceability, the satellite and weather API developer docs, the API sign-up and the Farmonaut apps.

▶ A walkthrough of satellite crop monitoring: reading NDVI maps to find stressed parts of a field to scout first. · 19:36

How we checked the facts

Every symptom, temperature and size in this guide comes from university extension pages or official documents: UC IPM, the University of Minnesota, UConn, Clemson, Penn State, Cornell and UF/IFAS. Copper limits come from EPA’s 2009 copper review and the EU Copper Task Force. The trial data come from the Plant Disease Management Reports of the American Phytopathological Society. Where sources differ, for example on bacterial spot size, we give both figures. We do not show photos, so use the table and the field check, and confirm unclear cases with a lab.

We cover a connected topic in Lemon Tree Black Leaves: 7 Solutions for Diseases.

FAQ

Are black dots on tomato leaves a fungus or bacteria?

It can be either. Septoria leaf spot and early blight are fungal. Bacterial speck and bacterial spot are bacterial. Tiny black dots inside a pale center point to Septoria. Small black spots with a yellow halo and no dots inside point to bacteria. Thrips, mites and sooty mold can also leave dark marks.

Is it Septoria leaf spot or early blight?

Look at the spot size and center. Septoria spots are small, under 1/8 inch, with a pale center and tiny black dots inside. Early blight spots are larger, 1/4 to 1/2 inch, with rings like a target. UMN, UConn Extension and UC IPM give these sizes. Both start on the lower leaves, and both can be present on one plant.

Should I remove leaves with black spots?

Yes, remove the worst lower leaves when the plants are dry, and bag or bury them rather than composting. Penn State suggests not removing more than 20% of a plant’s total leaf mass. Clean pruners between plants when bacteria are suspected.

Does copper cure black spots on tomato leaves?

No. Copper does not heal existing spots. It protects healthy leaves from new infections, and only partly, according to UC IPM. Spray before rain, follow the label’s per-spray and yearly limits, and combine copper with clean seed, drip irrigation and rotation.

Why do black spots start on the lower leaves?

Septoria and early blight survive on debris near the ground, and their spores splash up onto the oldest leaves. Penn State notes that low leaves dripping with morning dew are ideal for early blight. That is why mulch, staking and removing low leaves help. Bacterial diseases and insects can start anywhere on the plant.