Five fungal and fungus-like diseases account for most citrus damage in the U.S.: greasy spot, scab, melanose, Alternaria brown spot, and Phytophthora foot rot.
Greasy spot and melanose can look alike from a yard’s distance, and a black coating on leaves is often not a disease at all. Sorting out whether you’re looking at citrus tree fungus identification versus an insect problem starts with where the symptom sits — leaf surface, trunk bark, or feeder roots — because location narrows the cause faster than color ever will. Below, each disease gets a description you can match against your own tree.
What Do The Five Main Citrus Fungal Diseases Look Like?
Greasy spot shows swollen lesions on the lower leaf surface with yellow mottling above, and grapefruit may develop dark specks that merge into rind blotch. Citrus scab (Elsinoë fawcettii) starts as small pale-orange raised spots that harden into corky, wart-like growth, sometimes leaving a conical depression on the opposite leaf side. Melanose (Diaporthe citri) produces brick-red to black dots with a sandpaper texture on fruit, plus tiny dark depressions with yellow margins on young leaves. Alternaria brown spot causes crater-like fruit lesions. Phytophthora foot rot begins as gum droplets at or just above the bud union and can progress to brown, slippery, girdling bark.
| Disease | Where It Shows | Signature Look |
|---|---|---|
| Greasy spot | Lower leaf surface, fruit rind | Swollen lesions, yellow mottling above |
| Citrus scab | Leaves, young fruit | Corky wart-like raised growth |
| Melanose | Fruit, leaves, stems | Brick-red dots, sandpaper texture |
| Alternaria brown spot | Fruit | Crater-like sunken spots |
| Phytophthora foot rot | Trunk, crown, roots | Gumming, dark slippery bark |
| Sooty mold | Leaf and fruit surfaces | Black coating that scrapes off |
Is The Black Coating Fungus Or Something Else?
Sooty mold is surface fungus feeding on honeydew from whiteflies, aphids, mealybugs, or scale — so the black film traces back to insects, not to tissue infection. Deposits concentrate near the stem end and can be scraped off fruit. Treating the coating alone misses the source; the insects underneath are what needs attention.
Genuine tissue infections sit deeper. Melanose feels raised and rough. Greasy spot pairs leaf swelling with yellow mottling. Phytophthora rot on feeder roots leaves a soft, discolored cortex that sloughs away to expose a white central cylinder. That white core under slipping bark is one of the clearest confirmations you can get in the field.
Fruit blemishes also don’t guarantee spoiled insides. Much damaged fruit stays edible — check for rancid odor and soft decay before eating. When the diagnosis is ambiguous or you’re ready to treat, a fungicide choices for citrus tree treatment page can help match product to disease, though Phytophthora in particular resists foliar sprays because the pathogen lives in soil and bark.
How Should You Gather Evidence Before Treating?
Photograph the whole tree, the affected branch, both leaf surfaces, fruit, trunk, and the soil line — with a ruler for scale in each shot. Then log citrus type, irrigation habits, recent rainfall, drainage, freeze or heat damage, and whether symptoms come and go with the season.
Inspect the soil line and bud union for cracking, gum, dark water-soaked bark, or girdling. Dig into roots only when you must. Note that gum deposits alone don’t prove Phytophthora — drought, injury, salinity, nematodes, and root weevils all cause decline. Overwatering and poor drainage raise Phytophthora risk, and root rot often shows no clear aboveground sign at all.
For a definitive answer, submit samples to a state university extension plant clinic. The University of California’s citrus fungal disease reference and the University of Florida’s citrus diagnostic publications are both reliable starting points, and extension clinics can run pathogen-specific testing when symptoms stay ambiguous. Fungicides are product- and state-specific, so use only what’s registered for your crop and site and follow the current label exactly.
Common Questions
Will my citrus tree survive foot rot?
Early Phytophthora foot rot is manageable if caught before the bark lesion girdles the trunk. Once the rot fully circles the trunk, the tree usually declines beyond recovery. Check the soil line routinely, improve drainage, and avoid mounding soil against the bud union.
Can I eat fruit with melanose or scab spots?
Usually yes. Melanose and scab are rind blemishes that rarely reach the flesh. Inspect for soft decay, unusual odors, or mold before eating, and discard anything with signs of internal breakdown.
No. Greasy spot, scab, melanose, and Alternaria respond to different active ingredients and timing windows. Phytophthora needs soil-directed treatment rather than foliar spray. Match the product to the confirmed disease and your state’s registration rules.
Sources
- University of California, Riverside. “Fungal Diseases of Citrus” Supports disease descriptions for greasy spot, scab, melanose, and Alternaria.
- University of Florida IFAS. “Citrus Disease Diagnostic Guide” Supports Phytophthora symptom descriptions and diagnostic steps.
- University of Arizona Extension. “Citrus Diseases and Disorders” Supports root rot and trunk symptom guidance.