What Are the Causes of Brown Spots at the Base of Oranges?

Updated February 21, 2017

If your orange trees are bearing fruits with brown spots, your trees could have a disease or insect infestation. Several different fungal diseases can cause brown spots at the base of oranges, along with an insect culprit known as the citrus rust mite. In order to properly treat the problem, you must first identify the disease or other agent that's causing the brown spots. If you need to use a chemical like a fungicide or insecticide to treat your orange trees, be sure to follow the directions on the label exactly.

Alternaria Fruit Rot

Caused by the fungus Alternaria alternata, Alternaria fruit rot causes oranges to turn lighter in colour with brownish spots, according to the University of Arizona Cooperative Extension. Some oranges don't show any noticeable spots on the rind, but you'll see a brownish discolouration inside the fruits. The fungal disease is also called Alternaria brown spot, and it can ravage whole crops of oranges, says the University of Florida IFAS Extension. Alternaria fungi tend to grow on dead fruit tissues during rainy and humid weather, typically entering the oranges through splits in the fruits. Although no fungicides are available for effectively treating Alternaria infections, preventing fruit splitting by properly watering and fertilising the trees can keep the fungus from infecting your oranges.

Phytophthora Rot

Foot rots caused by Phytophthora species of fungi can affect the fruits of orange trees, in addition to the roots. When the fruits become infected, the disease is called brown rot. Orange trees with brown rot develop brown spots on the fruits, often during warm, wet weather in the summer and autumn. Phytophthora fungi thrive on water and poor air circulation, and the pathogens enter the orange trees through wounds in the fruits, trunk and other parts. Improving air circulation through pruning and keeping debris or mulches away from the trunk can help prevent Phytophthora infections, along with preventing wounds to the trees. You can also use a systemic fungicide made specifically for Phytophthora species to help eradicate the disease, applying the chemical to the crown, trunk and soil of the infected orange trees.

Citrus Canker

Citrus canker is a disease that causes brown lesions and spots on the fruits, stems and leaves of orange trees, according to Purdue University. Citrus canker can kill orange trees and is usually caused by Xanthomonas campestris or Phytomonas citri. In addition to brown spots on the fruits, you may also notice brown raised lesions on the leaves of your orange tree, says the Florida Department of Agriculture and Consumer Services. The lesions often have oily or water-soaked and yellow margins around them. Due to the highly contagious nature of citrus canker, many state and county governments require that you contact the local agricultural extension office if you suspect that your orange tree is infected. Consult your extension office for the proper treatment methods for citrus canker as well.

Sweet Orange Scab

Sweet orange scab is a common citrus disease caused by the fungus Elsinoe australis and is related to common citrus scab. The disease causes brownish-grey wart-like scabs or lesions on the oranges, usually attacking only young fruits within six to eight weeks of petal fall. To control sweet orange scab, you can spray your orange trees with a copper fungicide or another effective fungicide, such as pyraclostrobin, ferbam, thiophanate methyl, triflozystrobin or azoxytrobin. Fungicide sprayings for sweet orange scab are typically performed twice in the growing season, once at two-thirds petal fall and again about two to three weeks later.

Greasy Spot

Greasy spot is another common fungal disease of orange trees, causing brown to black greasy spots on orange leaves and fruits. Greasy spot tends to cause pinpoint dark spots on the orange rinds. Because the fungus that causes greasy spot grows on decomposing fallen leaves, you should remove and destroy all fallen leaves around your orange trees. You can also spray your infected orange trees using a copper-based fungicide or horticultural oil.


Melanose causes dark-brown, raised spots on the leaves and fruits on orange trees, sometimes appearing as "tear-streaking" on the oranges as the fungal spores drip down the rinds. Melanose lesions are rough in texture and, unlike greasy spot lesions, develop over the orange's oil glands. Melanose is most common in older or neglected orange trees, because the fungus enters through newly-dead twigs. If your orange tree has melanose, spray it with a copper fungicide twice each year about two to three weeks after petal fall and again two to three weeks after that.

Rust Mites

The effects of rust mites on orange trees can look similar to melanose and greasy spot diseases. Rust mites feed on the fruits and leaves, causing brown spots on the oranges and russeting of the leaves during humid summer weather. The tiny yellow wedge-shaped rust mites tend to feed in the shade, so you'll notice that the brown spots on the oranges are limited to areas where there isn't direct sunlight on the fruit. One treatment option for getting rid of rust mites on your orange trees is to introduce a beneficial fungus known as Hirsutella, which is a biological control for citrus rust mites.

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