Citrus Tree Diseases: From Greening to Root Rot, What's Hurting Your Tree

Citrus diseases fall into two categories: the ones you can manage yourself, and one you legally cannot. The one you can’t is citrus greening, also called Huanglongbing or HLB. There’s no cure, no spray, no resistant variety, and in many US counties homeowners are required to report suspected cases to the state. If you grow citrus in California, Florida, Texas, Arizona, Louisiana, or Georgia, learn the symptoms first.

The other diseases on this list (citrus canker, brown rot, sooty mold, melanose, foot rot) all respond to standard home-garden treatment: copper fungicide, decent sanitation, careful irrigation, and rootstock selection.

This guide covers all six. Where the regulatory situation matters (HLB and citrus canker in some states), the practical homeowner action is to contact your state department of agriculture, not to fight the disease alone.

How to tell which disease you’re looking at

Quick visual triage. Match the most obvious symptom and jump to the section below.

• Asymmetric blotchy yellowing on leaves, small lopsided fruit that stays green at the bottom: citrus greening (HLB), call your state agriculture department immediately
• Raised corky brown lesions with a yellow halo on leaves, twigs, and fruit: citrus canker
• Round brown soft rot on low-hanging fruit after winter rains: brown rot (Phytophthora)
• Black sticky soot covering leaves and fruit, with sticky honeydew underneath: sooty mold (from scale or aphids)
• Small reddish-brown raised pustules on leaves and fruit, sometimes in tear-drop patterns: melanose
• Bark cracking with dark gum oozing at the base of the trunk: foot rot / Phytophthora gummosis

Most citrus disease problems trace to soil moisture (too much), insect pressure (aphids/scale/psyllids), or a soil-splashed pathogen reaching the lower canopy. Get the rootstock right, manage irrigation, and prune up the skirt of the tree, and you’ll prevent more than half of what follows.

Citrus greening (HLB / Huanglongbing)

Citrus greening, also called Huanglongbing or HLB, is the disease threatening to wipe out the US citrus industry. It’s caused by a bacterium-like organism (Candidatus Liberibacter asiaticus), spread by the Asian citrus psyllid (Diaphorina citri). According to USDA APHIS, the disease has now been confirmed in Florida (statewide), Texas, California, Arizona, Louisiana, and Georgia, with quarantine zones expanding annually.

There is no cure. Infected trees decline over 3-7 years and die. The most important thing a homeowner can do is recognize the symptoms early and report them so the regional psyllid management program can respond.

What it looks like

The diagnostic symptom is asymmetric yellowing on the leaves, called “blotchy mottle.” Imagine a leaf with a yellow patch on the left side of the midvein and a green patch on the right side at the same height. That asymmetry is the key tell, because nutrient deficiencies (zinc, manganese, iron) produce symmetric patterns across the midvein.

Other signs:

• Small, lopsided fruit that develops a curved core
• Inverted color: the fruit stays green at the stylar end (the blossom end, opposite the stem) when it should be orange or yellow. This is where “greening” gets its name.
• Bitter, salty-tasting flesh in fruit that’s still attached to an infected tree
• Twig dieback and gradual decline of one quadrant of the canopy at a time
• Aborted seeds, often blackened, inside affected fruit

Why it happens

The Asian citrus psyllid is a small (1/8 inch) brown-mottled jumping insect that feeds on citrus tissue and transmits the bacteria during feeding. The psyllid prefers new flush growth, which is why HLB symptoms first appear on young leaves on rapidly growing shoots.

What to do about it

The homeowner playbook is short:

1. Photograph the symptoms carefully. Get clear shots of the asymmetric leaf mottling, the lopsided fruit, and the green-bottomed fruit.
2. Contact your state department of agriculture. In California, that’s CDFA (1-800-491-1899). In Florida, that’s FDACS. In Texas, that’s TDA. The state will send an inspector to confirm and decide on action.
3. Do not move plant material. Don’t move infected trees, don’t move citrus fruit out of quarantine zones, don’t share cuttings with friends.
4. Apply for psyllid treatment if available in your area. Several states have residential treatment programs that target the vector at no cost.
5. Once confirmed, remove the tree to prevent it from being a reservoir that infects neighboring citrus. Most state programs cover removal costs or coordinate the work.

Do not pursue copper sprays, fertilizer fixes, or “miracle cures” sold online. HLB has no available chemical cure. Any product that claims to cure HLB is at best supportive and at worst fraudulent.

How to keep it from coming back

If you’ve lost a tree to HLB, you can replant after a fallow period (usually 30 days under most state programs). New trees must come from a certified disease-free nursery (look for the state Citrus Nursery Stock Certification Program seal). Any new citrus should also receive psyllid monitoring and possibly treatment, especially in active quarantine zones.

Citrus canker

Citrus canker is caused by the bacterium Xanthomonas citri subsp. citri. Like HLB, it’s a regulated disease in Florida, Texas, and the Caribbean territories, though Florida’s eradication program ended in 2006 and tree removal is now voluntary. The disease is geographically restricted, so most US citrus growers outside of the Gulf states never see it.

What it looks like

Raised corky lesions on leaves, twigs, and fruit. Per UF/IFAS, young lesions appear as raised pustules on both leaf surfaces (more prominently on the lower surface). As they mature, the pustules become corky with raised margins, sunken centers, and a surrounding yellow halo. Severe infection causes premature leaf drop, premature fruit drop, and twig dieback.

Susceptibility varies by cultivar:

• Highly susceptible: grapefruit, Mexican lime, early oranges (Hamlin, Pineapple)
• Moderately susceptible: lemons, regular limes, Navel oranges
• Less susceptible: Valencia oranges, tangors, tangelos, mandarin hybrids
• Most resistant: tangerines

Why it happens

The bacteria multiply in warm wet weather and spread via wind-blown rain. Hurricane events famously redistribute citrus canker across hundreds of miles in a single storm, which is one reason Florida’s eradication program was abandoned.

What to do about it

In Florida and Texas, removing infected trees is voluntary but still recommended to slow spread. Outside of quarantine zones, citrus canker is rare enough that any suspicious lesion should be reported to the state for confirmation.

For management on confirmed canker trees:

• Copper spray applications during wet weather suppress the disease. Standard rates from Bonide Copper Fungicide at full label rate, applied every 3 weeks during wet weather, reduce new infections.
• Don’t move plant material. Decontaminate tools and clothing with quaternary ammonium disinfectant.
• Wind protection with hedges or fencing reduces wind-driven rain spread.
• Avoid overhead watering. Drip or basin irrigate at the root zone.

Brown rot (Phytophthora)

Brown rot of citrus is caused by several species of Phytophthora (water molds, technically not true fungi). It hits low-hanging fruit during cool wet winters, especially in California and other Mediterranean climates. Per UC IPM brown rot of citrus, the pathogens “persist in and spread from soil,” so fruit near ground level is the primary target.

What it looks like

A small leathery brown spot appears on the side of an affected fruit, usually near the bottom of the tree where soil splash reaches. Within a few days, the spot expands across the whole fruit, which softens, develops a distinct musty odor, and may show a faint white mold on the surface in humid conditions. Infected fruit drops to the ground and rots completely.

Brown rot is mostly a fruit disease. Leaves and twigs are rarely affected.

Why it happens

The pathogen lives in the soil and waits for cool wet weather. According to UC IPM, infection occurs at 57-73°F after 3 hours of continuous wetness. The trigger is rainstorm splashing: drops hit infested soil, bounce up to low-hanging fruit, and deposit zoospores on the fruit surface. From there, brown rot expresses within days.

What to do about it

Two interventions handle most cases.

• Prune the tree skirt up at least 2 feet above the ground. This is the single highest-leverage prevention. No low-hanging fruit means no soil-splash infection. UC IPM specifically recommends 24+ inches of clearance from soil to lowest foliage.
• Preventive copper spray before the first fall rains. A single application of copper fungicide or fosetyl-al on the lower 4 feet of canopy and the soil beneath protects the high-risk zone through the rainy season.

Post-infection treatment isn’t worth pursuing. By the time you see brown rot on a fruit, the rest of the season’s protection has already failed. Pick up and bag dropped fruit immediately so the spore load doesn’t build up for next year.

Sooty mold

Sooty mold is the dark, soot-like black coating on citrus leaves and fruit that worries most first-time growers. It looks dramatic and it cleans off easily. The mold itself is harmless. The problem is what’s causing it.

What it looks like

A flat black coating on the upper surface of leaves and on the fruit skin, often coinciding with sticky honeydew dripping from the canopy onto whatever is parked underneath the tree. The mold doesn’t penetrate the leaf tissue. It just grows on the sugary honeydew that scale insects, aphids, mealybugs, or whiteflies excrete.

Why it happens

Sooty mold is a downstream symptom of insect feeding. The insects (most commonly soft brown scale, citrus mealybug, or aphids on new growth) suck sap from the tree and excrete the excess sugar as honeydew. The honeydew drips onto lower leaves, where airborne mold spores colonize the sticky surface and grow into the black film. Solve the insect problem and the mold disappears with the next rain.

What to do about it

The fix is to kill the insect, not the mold. For most citrus, that means:

• Horticultural oil or neem oil spray in spring and again in fall. Bonide Neem Oil concentrate is the home-garden standard and runs $15-30 a bottle. Mix per label and spray the underside of leaves where scale and aphids feed.
• Encourage beneficial insects. Lady beetles, lacewings, and parasitic wasps keep scale and aphid populations in check. Don’t blanket-spray broad-spectrum insecticides on citrus, since they kill the beneficials too.
• Once the insects are gone, sooty mold sloughs off naturally within a few weeks. Gentle rinsing with the hose speeds the cleanup if the tree is small enough.

Melanose

Melanose is caused by Diaporthe citri. It produces small, reddish-brown, raised pustules on leaves and fruit, sometimes arranged in distinctive tear-drop or mud-cake patterns where rain has streaked spores down the fruit. The disease is cosmetic on most cultivars but can be severe on grapefruit, which makes it a commercial problem in Florida.

What it looks like

Small (1-2 mm) reddish-brown raised spots on leaves, with a yellow halo when fresh. On fruit, lesions are reddish-brown, rough to the touch, and can spread into characteristic streak patterns where rain has carried spores down the fruit surface. Affected fruit is edible but uglier than perfect.

Why it happens

The fungus lives in dead wood on the tree. Per the research on Diaporthe citri, pycnidia (fungal fruiting bodies) develop on dead branches, especially after rain, and release conidia as slimy masses. Raindrops carry the conidia to nearby leaves, twigs, and fruit. Persistent rains and warm weather favor disease development.

What to do about it

• Remove dead wood from the tree every winter. Dead branches and pruning debris on the ground are the spore source. A clean tree has minimal melanose.
• Copper fungicide during the wet season suppresses new infections. Bonide Copper Fungicide at label rate, applied during periods of frequent rain, gives a clean fruit harvest.
• Cultivar selection matters for new plantings. Grapefruit is the most susceptible. Other citrus (oranges, mandarins, lemons) are less prone.

For most backyard growers in the West (California, Arizona), melanose is rare enough to not need preventive spraying. In the Southeast and Gulf states where humid summers drive the disease, copper applications during wet weather are standard practice.

Foot rot / Phytophthora gummosis

Foot rot, also called Phytophthora gummosis, is the trunk disease most likely to kill a backyard citrus tree. It’s caused by the same Phytophthora species that produce brown rot in the fruit, but the trunk infection is far more serious. According to UC IPM Phytophthora gummosis of citrus, lesions can expand around the trunk circumference and girdle the tree within months or years.

What it looks like

Dark, water-soaked patches on the bark of the lower trunk, often with sticky brown or dark gum oozing from small cracks. The bark may smell sour or fermented underneath. As the disease progresses, the bark cracks open more widely, exposing pinkish or brownish inner tissue. The leaves of the affected tree may show progressive yellowing and dieback, but the trunk symptom is usually the first sign.

Don’t confuse foot rot with normal citrus bark cracking, which is common on older trees and not associated with gum or rot underneath.

Why it happens

The pathogen requires moist soil and direct contact with susceptible bark. The most common triggers:

• Soil mounded against the trunk (mulch, dirt, or grass) keeps the bark wet and lets soil-borne Phytophthora infect through lenticels and small wounds.
• Susceptible rootstocks: sour orange rootstock, especially, is highly vulnerable. Trifoliate orange and citrange rootstocks resist foot rot.
• The graft union below soil level, which puts the susceptible scion wood in contact with soil-borne pathogens.
• Overhead irrigation wetting the trunk during cool weather creates ideal infection conditions.

What to do about it

Caught early, foot rot can be managed. Caught late, the tree is finished.

• Scrape away the affected bark with a sharp clean knife, removing all dark or wet-looking tissue and continuing into healthy light-brown bark with a 1-2 inch buffer.
• Let the exposed wood dry for a day in dry weather, then paint with copper fungicide or fosetyl-al.
• Repeat if the disease returns the following season.
• Fix the underlying conditions: pull mulch and soil at least 6 inches away from the trunk, raise the graft union above soil level if possible, switch from overhead to drip irrigation.
• Test soil drainage before suspecting foot rot. A Luster Leaf Rapitest Soil Test Kit can confirm pH and nutrient issues, but the field test that matters most is drainage: dig a 1-foot hole, fill with water, see how long it takes to drain. Less than 4 hours is good. More than a day means you have a drainage problem driving Phytophthora pressure.

How to keep it from coming back

Rootstock matters most. If you’re planting new citrus in a region with foot rot history, ask the nursery which rootstock the tree is grafted on. Trifoliate orange, citrange, and Alemow rootstocks resist Phytophthora. Sour orange (the historical standard in Florida) is highly susceptible.

For container citrus and indoor citrus trees, well-draining potting mix and bottom-watering practices prevent most foot rot. The disease is mostly a landscape problem, not a container problem, but waterlogged containers do produce it occasionally.

When to call your state department of agriculture

Two situations require contacting state authorities rather than treating yourself.

First, suspected citrus greening (HLB) at any time, in any state where the disease has been confirmed. The symptoms (asymmetric blotchy mottle on leaves, lopsided fruit that stays green at the bottom) require state inspector confirmation, and homeowner-reported cases are part of how state psyllid management programs decide where to focus treatment.

Contact numbers:

• California: CDFA Pest Hotline, 1-800-491-1899
• Florida: FDACS Division of Plant Industry, 1-888-397-1517
• Texas: TDA Citrus Office
• Arizona, Louisiana, Georgia: contact your state department of agriculture’s plant pathology section

Second, suspected citrus canker in any region outside Florida or Texas where it’s not previously been confirmed. New geographic detections are tracked nationally and reporting matters.

For everything else (brown rot, sooty mold, melanose, foot rot), the homeowner can handle the diagnosis and treatment with standard tools.

When to call an arborist

For non-regulatory citrus problems, two situations warrant a paid visit. First, a mature backyard citrus showing decline across multiple branches where the underlying cause isn’t obvious (foot rot, root rot, nutrient deficiency, or freeze damage). Second, a zone 9 or zone 10 backyard citrus that’s been in the family for decades and is the most valuable tree on the property.

An ISA-certified arborist consultation runs $75-200 in most US markets. Find one through the Trees Are Good arborist locator or read our guide to what an arborist does before you call.

Prevention checklist

Eight habits cover most citrus disease problems:

• Buy from a certified nursery. Any new citrus should carry the state Citrus Nursery Stock Certification seal. Free of HLB, free of citrus canker, free of viruses.
• Pick a resistant rootstock. Trifoliate orange, citrange, or Alemow for foot-rot-resistant planting. Avoid sour orange in regions with Phytophthora pressure.
• Plant on raised mounds in heavy soils or anywhere with drainage uncertainty. Even a 6-8 inch raised crown reduces foot rot risk significantly.
• Keep mulch 6 inches away from the trunk. No mulch volcanoes. Soil contact with bark is foot rot’s entry route.
• Prune the skirt up 2+ feet above the ground. Stops brown rot on low-hanging fruit and reduces soil-splash pathogen pressure.
• Drip or basin irrigate at the root zone. Don’t wet the trunk or canopy during cool weather. Overhead irrigation is the easiest preventable cause of citrus disease.
• Monitor for psyllids in HLB regions. Yellow sticky cards or visual inspection of new growth flushes catches Asian citrus psyllids early.
• Single copper application before fall rains in regions with brown rot or melanose pressure. One well-timed spray does more than a season of poorly timed ones.

For nutrient timing through the season that supports tree vigor without overstimulating soft growth, see our fruit tree fertilizer guide and this seasonal fertilizing guide on mklibrary.com.

For broader fungal disease patterns across the rest of your yard, see our tree fungus guide.

Frequently asked questions

What is the most dangerous citrus tree disease?

Citrus greening (HLB) is the most dangerous and the one with no cure. Foot rot (Phytophthora gummosis) is the most dangerous non-regulatory disease and can kill a tree within 1-3 years of trunk infection. Citrus canker is dangerous in regulated regions but rarely fatal. Brown rot, sooty mold, and melanose are manageable problems that rarely kill trees.

Can I save a tree with citrus greening?

No. HLB has no cure. Infected trees decline and die within 3-7 years. The best response is to confirm the diagnosis through your state agriculture department and remove the tree promptly to prevent it from infecting neighboring citrus.

Why are my citrus leaves turning yellow?

Several causes:

• Asymmetric blotchy yellowing: HLB (call your state agriculture department)
• Symmetric vein yellowing: iron, zinc, or manganese deficiency. Apply a balanced citrus fertilizer.
• Yellowing with overall decline: possible foot rot, root rot, or overwatering. Check the trunk base and soil drainage.
• Yellow older leaves dropping while new growth stays green: normal seasonal leaf turnover. No action needed.

Should I spray copper on my citrus tree every year?

In humid regions with regular brown rot, melanose, or citrus canker pressure: yes, one copper application before fall rains is a good preventive practice. In dry regions (California outside the coast, Arizona, dry interior Texas), copper is usually unnecessary unless you’re seeing active disease.

My citrus tree has black sticky stuff on the leaves. Is it dying?

No. That’s sooty mold growing on honeydew from scale insects, aphids, or mealybugs. The tree itself is fine. Treat the underlying insect with horticultural oil or neem oil, and the mold disappears within a few weeks.

Can I plant citrus in zone 7 or 8?

Hardy citrus (kumquat, satsuma mandarin, yuzu, Meiwa kumquat, Bouquet de Fleur sour orange) can survive in zone 8 with protection. True sweet oranges, lemons, and limes need zone 9 or warmer. For zone 7 and below, citrus must be grown in containers and moved indoors for winter, in which case our best indoor trees guide covers the indoor care requirements.

What’s the difference between brown rot and foot rot?

Both are caused by Phytophthora species, but they attack different parts of the tree. Brown rot attacks low-hanging fruit during wet winter weather and produces a soft brown decay with a musty odor. Foot rot attacks the trunk at or below the soil line and produces bark cracking with dark gum exudate. Both share the same prevention strategies (good drainage, drip irrigation, raised planting), but foot rot is the one that kills trees while brown rot mostly ruins fruit.

Is there a quarantine restriction on moving citrus fruit?

Yes, in HLB and citrus canker regulated areas. USDA APHIS maintains quarantine zones in California, Florida, Texas, Arizona, Louisiana, and Georgia. Moving citrus plant material (trees, cuttings, budwood) across quarantine boundaries is restricted, and in some cases moving fruit out of regulated counties requires inspection. Check the USDA APHIS citrus quarantine map before bringing citrus fruit from one region to another, especially when traveling.