Brown spots on lemons are common, but in the vast majority of cases, these markings are purely cosmetic damage to the outer rind. They do not penetrate the fruit to affect the flavor, juice, or internal pulp. The spots result when the skin cells are damaged by disease, pests, or environmental stress, causing the fruit to form a protective, corky layer over the injury. Understanding the distinct appearance of these spots is the first step toward accurately diagnosing and resolving the underlying issue on the tree.
Fungal and Bacterial Causes
Many brown blemishes result from fungal diseases that thrive in warm, humid conditions when moisture lingers on the fruit’s surface.
Citrus Melanose, caused by the fungus Diaporthe citri, manifests as small, dark brown to black spots that are raised and rough, giving the rind a sandpaper-like texture. Melanose is associated with dead or decaying wood within the tree canopy, where the fungal spores develop. Spores are primarily dispersed by water splash from rain or overhead irrigation onto young fruit. Heavy infection may cause spots to merge into larger, cracked patches known as “mudcake melanose,” or form streaks called “tearstain melanose.”
Citrus Scab, caused by Elsinoe fawcettii, produces raised, irregular, wart-like lesions that are initially pinkish but darken to a grey or brown corky texture. Scab lesions are typically more pronounced than Melanose and often distort the shape of the lemon if infection occurs on very young fruitlets. The fruit is susceptible to Scab infection from half petal-fall until it reaches approximately 1.5 inches in diameter, requiring a continuous wet period for spores to germinate.
Damage from Pests
Minute insect and mite activity on the surface of young lemons causes permanent scarring that appears as brown or silvery blemishes on the mature fruit.
Citrus Rust Mites are microscopic pests that feed on the surface cells of the rind, typically on fruit half an inch or larger. Their feeding action destroys the rind cells, resulting in a silvery or reddish-brown discoloration often termed russeting. This damage is purely superficial and does not impact the internal juice quality.
Citrus Thrips leave a characteristic, patterned brown scarring. Immature thrips feed in sheltered areas, particularly under the calyx, or “button,” at the stem end of the fruit, causing a distinct ring-shaped scar to form. As the lemon grows, this ring-shaped scar expands outward, leaving a band of scabby, gray or silvery tissue around the stem.
Scale insects, such as California red scale, are sap-sucking pests that can also lead to discolored flecks or mottling on the rind. The feeding damage to the epidermal cells leaves permanent brown spotting. Additionally, sooty mold, a black, superficial fungus that grows on the sugary honeydew excreted by scale and other sucking pests, can contribute to a spotted appearance.
Environmental and Physical Stressors
Brown spots can also result from environmental factors, which are often distinguishable by the pattern of the damage.
Sunburn, or sunscald, occurs when a lemon is suddenly exposed to intense, direct sunlight, especially in temperatures exceeding 95°F (35°C). This damage typically appears as a large, localized area of darker yellow or golden-brown discoloration on the side of the fruit facing the afternoon sun. The affected area is often hardened or flattened.
Physical abrasion, commonly called wind rub, is a mechanical injury occurring when young fruitlets are whipped against neighboring leaves, branches, or thorns by strong winds. The resulting injury heals with a protective layer of corky tissue. This appears on the mature lemon as transverse, grayish-buff colored scars across the surface. This type of scarring is generally limited to the early stages of fruit development, within the first 12 weeks after the petals fall.
Cold or freeze damage causes brown spots that may initially appear water-soaked before developing into dark, reddish-brown depressions or pitting. External spots indicate that the internal juice vesicles may have ruptured. When internal vesicles are damaged, the lemon’s pulp dries out, and the fruit becomes hollow and light for its size.
Management and Prevention Strategies
Successful management of brown spots requires an accurate diagnosis, as treatment for fungal disease differs significantly from pest infestation or environmental damage.
Managing Fungal Diseases
For fungal causes like Melanose and Scab, the primary cultural practice is removing the source of the fungal spores. This involves regular pruning to eliminate all deadwood, twigs, and weak branches from the tree canopy, as pathogens overwinter and reproduce there. Improving airflow within the canopy through strategic pruning also helps the fruit dry more quickly, which is less favorable for fungal growth. Targeted treatments often involve the use of copper-based fungicides, which act as a protective barrier on the fruit’s surface, preventing spores from germinating. The most effective application window is during periods of high humidity and rainfall, especially when the fruit is young and most susceptible, typically starting at petal fall.
Controlling Pests
Intervention for pest-related scarring focuses on controlling the insect or mite population during the susceptible period of fruit development. Horticultural oils or insecticidal soaps are highly effective against soft-bodied pests like mites and thrips. These treatments must be applied thoroughly to target active populations on new growth and developing fruit. Timing is important, particularly for thrips, where control measures should be applied shortly after petal fall to protect the tiny fruitlets before the characteristic scarring occurs.
Preventing Environmental Damage
Environmental damage requires cultural adjustments to protect the fruit from extremes. To prevent sunburn, maintain a dense, healthy leaf canopy through proper irrigation and fertilization, as the leaves naturally shade the fruit. In high-risk, arid climates, growers may apply a protective coating, such as a kaolin clay product, which creates a white film to reflect the sun’s radiation and reduce the rind temperature. Installing windbreaks or strategic pruning to remove interior thorns and prevent branch rubbing minimizes physical abrasion, significantly reducing wind rub scars.