Lemon Tree Fungus: 8 Diseases and Fungicide Rates

Lemon tree fungus is usually one of eight diseases: greasy spot, melanose, citrus scab, anthracnose, Phytophthora (brown rot, gummosis and root rot), Alternaria rot, citrus black spot or, around the Mediterranean, mal secco. For most of the leaf and fruit spots, the standard fungicide for a lemon tree is a fixed copper spray: UF/IFAS puts a typical dose at about 2 lb of metallic copper per acre per spray, and says no more than 8 to 12 lb a year should be needed on large trees. Phytophthora is different and is managed with drainage, skirt pruning, copper and phosphonate products.

Below: how to tell the diseases apart, which fungicide works on each, when to spray, and the label limits. A calculator turns a copper rate into product and cost for your own block. If you are planting a new block, start with our guide on how to grow a lemon tree orchard.

Lemon tree fungus at a glance: eight diseases

The table sums up the fungal and fungus-like diseases that most often hit lemons. The sources behind each line are in the sections below.

Sooty mold is left out on purpose: it grows on insect honeydew, not inside the tree (see the look-alikes below).

1. Greasy spot

Greasy spot is caused by the fungus Zasmidium citri-griseum. Yellow spots show on top of the leaf, then brown blisters on the underside turn dark and greasy, and badly hit trees shed leaves.

The Florida guide on greasy spot says spores are mainly released from April to early June and that infection conditions run from June through September. Leaves can be infected at any age. One oil or copper-plus-oil spray from mid-May to June gives acceptable control on processing Valencia oranges, and copper controls it more consistently than oil.

2. Melanose

Melanose is caused by Diaporthe citri. It shows as tiny, raised, dark brown specks on fruit, leaves and twigs that can run together into a rough crust and downgrade fresh fruit.

The Florida melanose guide explains that spores come from dead twigs 1/8 to 1/4 inch thick inside the canopy, mostly ones that died in recent months, and rain splashes them onto young fruit. Living leaves and fruit produce none. So prune out dead wood first, then protect young fruit with copper.

3. Citrus scab

Scab is caused by Elsinoë fawcettii. It starts as small pink to light brown pustules on young leaves, shoots and fruit that grow into cracked, wart-like scabs. UF/IFAS notes that the warts on lemons stand up more than the flatter lesions on grapefruit, which can be mistaken for wind scar.

Young tissue is the target. Where last season’s leaves were badly scabbed, the UF/IFAS home citrus guide suggests three copper sprays: at about one-quarter expansion of the spring flush, at petal fall, and about three weeks later. Fruit becomes resistant two to three months after petal fall.

4. Anthracnose

Anthracnose is caused by Colletotrichum gloeosporioides. It causes twig dieback, early leaf drop and “tear stain” streaks where spores drip onto fruit in wet or foggy weather. It mainly affects stressed trees with old dead wood, and only occasionally lemons. The UC IPM anthracnose guidelines say it is usually not severe enough to need preventive sprays; if you do spray, cover the whole tree in the fall. Insecticidal soaps can make it worse by damaging the rind wax.

5. Phytophthora: brown rot, gummosis and root rot

Phytophthora is a water mould, not a true fungus, but it lives in the soil of almost every citrus orchard and causes three problems:

• Brown rot of fruit. Tan to olive-brown, leathery, strong-smelling patches on fruit near the ground, after rain splashes soil onto the low branches.
• Gummosis or foot rot. Sap oozing from small cracks in the trunk bark, which dries, cracks and peels. The lesion slowly circles the trunk.
• Root rot. Feeder roots rot, leaves turn light green or yellow, and the tree declines slowly.

The UC IPM gummosis guidelines say that if half or more of the trunk or crown of a mature tree is girdled, replacing the tree may cost less than trying to save it. Early signs are hard to spot, so inspect the lower trunk several times a year and keep the bud union above the soil.

6. Alternaria rot

Alternaria brown spot, the leaf and fruit spot disease, mainly hits mandarin hybrids such as Minneola tangelos and Murcott. On lemons the problem is Alternaria rot: fruit colours early and softens, mostly in storage. The UC IPM Alternaria rot guidelines say preharvest sprays usually do not work. Avoid tree stress so fruit does not split; packers use postharvest treatments.

7. Citrus black spot

Citrus black spot is caused by Phyllosticta citricarpa. Its typical “hard spot” is a round, sunken lesion up to 0.4 inch (10 mm) across with a grey centre and a brick-red to black edge, seen as fruit colours. The Florida citrus black spot guide says lemons are reported to be even more susceptible than oranges elsewhere. Spores sit in leaf litter; in Florida, monthly copper or strobilurin sprays run from May to mid-September. It is a regulated disease: in the US it is known only in Florida, which has quarantine areas, and the EU lists it as a quarantine pest (EPPO A1 list) (see also the EPPO datasheet for Phyllosticta citricarpa), so report suspect fruit to your plant health agency.

8. Mal secco

Mal secco is a vascular wilt caused by Plenodomus tracheiphilus. The EPPO datasheet says lemon is its main host and that it is present in most countries around the Mediterranean and in some bordering the Black Sea. It enters through wounds and spreads in the wood, so shoots wilt and die back. EPPO says pruning diseased shoots as soon as symptoms show and removing suckers and dead trees keep it in check. Chemical control is rarely used outside nurseries, and mancozeb was not approved in the EU as of March 2024.

▶ Spots, aphids and black growth on lemon and citrus leaves, and how to tell pest damage from disease. · 10:52

Lemon tree fungus look-alikes

Not every black or spotted leaf is a fungal infection. Check these first:

• Sooty mold. A black, wipe-off coating on leaves and fruit. It grows on honeydew from aphids, soft scales, mealybugs and whiteflies. The UC IPM sooty mold pest note says it does not infect the plant, though it blocks light, and it fades once the honeydew stops. Treat the insects, not the mold. The fruit is still edible after a wash.
• Copper injury. UC IPM warns that Septoria spot can be confused with copper injury. Copper sprayed in hot, dry weather can also spot fruit, which looks like a disease.
• Leaf miners and nutrient problems. Winding tunnels in young leaves are citrus leafminer, not a fungus. Yellow patterns between the veins can point to a nutrient shortage.
• Citrus greening (HLB). Blotchy yellow leaves and lopsided, bitter fruit can be huanglongbing, a bacterial disease spread by the Asian citrus psyllid. No fungicide helps; report suspect trees to your local agriculture office.

When unsure, send a sample to a plant clinic. UC IPM notes that root rot symptoms are often hard to tell apart from nematode, salt or flooding damage without a lab test.

▶ Citrus greening: the symptoms, the psyllid that spreads it, and control options. It is a bacterial disease, so fungicides do not help. · 13:17

Fungicide for lemon trees: what works on each disease

The FRAC code on a label tells you how the product works, which matters for resistance. These are the main groups in the UC IPM and UF/IFAS citrus guidelines.

Pick by disease and season, not brand. Follow the product label and local rules: the label sets the legal rate, spray count, intervals and where it may be used. Ask your extension service or a licensed adviser if unsure.

Copper: rates and yearly totals

Copper is the workhorse because it is cheap, works on many diseases and has low resistance risk. The UF/IFAS figures are the clearest public numbers:

• About 2 lb of metallic copper per acre per spray usually controls greasy spot and scab, and about 2 lb per acre for each three-week period protects fruit from melanose (UF/IFAS).
• For melanose on large trees, no more than 8 to 12 lb of metallic copper a year should be needed, even if copper is also used for scab, canker or greasy spot (UF/IFAS).
• From May to September, spray copper only when temperatures are moderate (below 94°F, about 34°C), at no more than 2 lb of copper metal per acre, without oil, and in at least 125 gallons of water per acre, to avoid spotting the fruit.

“Metallic copper” is the copper metal content, not the weight of product. A product that is 40% metallic copper needs 5 lb of product to deliver 2 lb of copper. Copper soap liquids are much weaker: the EPA-accepted label for Cueva copper soap gives 0.34 lb of metallic copper per gallon. For citrus it says to spray one to three weeks after petal fall, repeat every two weeks if necessary until fruit is 3 inches across, and not reapply within 7 days.

Plan for two side effects. A UF/IFAS whitefly fact sheet notes that copper also suppresses the “friendly fungi” that kill whiteflies, so whiteflies can increase. And copper builds up in soil: USDA’s National Organic Program allows fixed coppers and copper sulfate in organic crops only if they are used in a way that keeps soil build-up to a minimum.

Bordeaux mixture or fixed copper?

The UC IPM Bordeaux pest note describes Bordeaux (copper sulfate, lime and water) as longer lasting in winter rain but harsher on leaves, and it stains. Fixed coppers are easier to mix and gentler on new growth but less persistent. UC IPM lists Bordeaux for lemon brown rot only where there is no history of copper injury.

Strobilurins and resistance

Strobilurins (FRAC 11) suit hot months when copper could mark fruit; one late May or early June spray covers melanose and greasy spot. The greasy spot guide says not to use a strobilurin more than once a year for greasy spot, and the scab guide says not to use FRAC 11 products twice in a row. In California, UC IPM advises no more than one application of FRAC groups 1, 4, 9, 11 or 17 before rotating to another group.

Phosphonates and mefenoxam for Phytophthora

For brown rot, UC IPM lists fixed copper first, then fosetyl-Al (Aliette) at 5 lb per acre and potassium phosphite at 2 quarts per acre, each limited to four applications a year, plus oxathiapiprolin. Phosphonates can be sprayed on leaves and fruit or applied to soil. Mefenoxam (Ridomil Gold) is a soil treatment, used at planting, on resets and on bearing trees, timed to root growth flushes.

Re-entry and harvest intervals

Every label sets a restricted-entry interval (REI, hours before workers may go back in without protective gear) and a preharvest interval (PHI, days from the last spray to picking). UC IPM notes that when the REI is longer than the PHI, the longer interval is the minimum wait before harvest. For tank mixes, follow the most restrictive label.

Chart

Preharvest interval for selected citrus fungicides

Days from last spray to harvest, selected products from UC IPM citrus treatment tables (California)

When to spray lemon trees for fungus

Timing depends on when your rain falls. Fungicides protect; they do not cure old lesions. So the spray has to be on the tissue before the wet period that spreads the spores.

Infographic

Deciding on a lemon fungicide spray in 5 steps

1. 1Name the problemMatch the symptom to a disease, or send a sample to a lab.
2. 2Fix the causeDrain wet soil, lift the skirt and cut out dead wood first.
3. 3Pick the groupCopper for most spots; phosphonates for Phytophthora.
4. 4Time it to the rainSpray before the wet spell that spreads spores, on dry leaves.
5. 5Check the labelRate, spray count, copper total, REI and PHI.

Spray only when leaves are dry and rain is not expected soon. The University of Nevada, Reno oil guide adds that oil should not go on when temperatures are in the 90s °F, on drought-stressed trees or on new transplants.

How much is at stake on a lemon orchard

USDA’s Citrus Fruits summary put the value of US lemon production at about $749 million in the 2025-26 season from 62,500 bearing acres, or roughly $12,000 per bearing acre at packinghouse-door prices. That is an average across the crop, not a figure for your farm.

Chart

Value of lemon production per bearing acre

US dollars per bearing acre, 2025-26 season, packinghouse-door basis; value divided by bearing acres

California grew 26.0 million of the 27.6 million US boxes in 2025-26, at 475 boxes per bearing acre. Arizona fell to 212 boxes from 329; USDA gave no cause, so do not read it as a disease effect.

Chart

Lemon yield per bearing acre

Boxes per bearing acre, California and Arizona, three seasons

Copper spray calculator for lemon trees

Turn a copper rate into product, cost and a season total to check against the 8 to 12 lb per acre UF/IFAS figure. Take the metallic copper percentage from your label. The break-even line shows what share of your crop value the program must protect to pay for itself.

Try the numbers for your own farm below.

How to prevent lemon tree fungus

Lemon fungal diseases start with water, wounds or dead wood. These steps come from the UC IPM and UF/IFAS guidelines:

1. Plant high and drain well. Plant on a berm or high enough that the first side roots are just covered.
2. Water the roots, not the trunk. Avoid over-irrigation and fix poor drainage.
3. Lift the skirt. Prune low branches to 24 inches or more above the ground so rain cannot splash soil and Phytophthora spores onto fruit.
4. Cut out dead wood. Dead twigs feed melanose, anthracnose and mal secco. Prune after freezes and storms, cut below stained wood and clean tools between trees.
5. Keep the bud union clear. Pull soil and mulch back from the crown and lift tree wraps to check for gum.
6. Buy clean trees on tolerant rootstocks. UC IPM lists trifoliate orange, Swingle citrumelo, citrange, Alemow and sour orange as the most tolerant of Phytophthora root rot. Inspect new trees before planting.
7. Control honeydew insects. Fewer aphids, soft scales and mealybugs mean no sooty mold.
8. Clear fallen fruit and leaf litter where black spot or brown rot is a risk.
9. Scout on a schedule. Walk the block after every long wet spell and before each planned spray.

On larger blocks, satellite crop monitoring can show which parts of the orchard lose canopy vigour first, so you know where to walk. Farmonaut Satellite + AI Farm Monitoring System maps vegetation change for each field; it shows where trees are stressed, not which disease is the cause, so a ground check is still needed.

For a broader look at treatments, including bacterial and viral problems, see our guide to lemon tree disease and treatment.

▶ A walkthrough of satellite crop monitoring: reading NDVI maps to see where a field or orchard is under stress. · 19:36

How we checked the facts

Every rate, timing and limit here comes from UC IPM, the 2026-2029 Florida Citrus Production Guide (UF/IFAS), EPPO, an EPA-accepted label, USDA’s National Organic Program or USDA NASS. Product names are examples, not endorsements. Rates differ by country and product, so your label always wins.

We cover a connected topic in Harvesting Potatoes for Storage: Prevent Dry Rot.

FAQ

What is the best fungicide for a lemon tree?

For leaf and fruit spots, fixed copper, at about 2 lb of metallic copper per acre per spray (UF/IFAS). For Phytophthora, phosphonates such as potassium phosphite or fosetyl-Al are also used. Follow the product label and local rules.

How do I treat white fungus on a lemon tree?

White, fluffy or waxy spots on lemon leaves are often insects, not fungus: cottony cushion scale, mealybugs or whitefly. Look for sticky honeydew. Treat the insects with a water spray, horticultural oil or natural enemies.

How many times a year can I spray copper on lemons?

There is no single number; the label sets the rate, the interval between sprays and any yearly cap. As a guide, UF/IFAS says no more than 8 to 12 lb of metallic copper per acre a year should be needed on large trees. The Cueva copper soap label says not to reapply within 7 days on citrus.

Can a lemon tree recover from fungus?

Usually, for leaf and fruit spots, though marked leaves and rind stay marked. Gummosis is more serious: UC IPM says scraping out the diseased bark and letting it dry can halt it, but if half or more of a mature trunk is girdled, replacing the tree may be cheaper.

Is fruit with sooty mold or black spots safe to eat?

Fruit with sooty mold is safe after a wash with mild soap and warm water, according to UC IPM. Black spot and melanose mostly mark the rind; UF/IFAS says black spot lesions rarely cause internal rot. Throw away fruit with soft rot.

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