Onion Diseases and Controls


Onions and garlic are relatively pest free but there are three pests which could give you some problems, especially if you grow large quantities of bulbs. Basic pest management information is presented in the following:

Onion fly (onion maggot)

The onion fly prefers seed onions to multiplier onions. It will attack multiplier onions when grown in large quantity. Prevention is the best method of control. Never grow onions in the same location repeatedly: rotate with other crops. Use a minimum three year rotation and quickly compost onion debris, otherwise you run the risk of substantial crop loss. The onion fly is most likely to cause problems when 2 or 3 wet growing seasons occur in a row. Relatively dry growing seasons tend to inhibit the fly. Garlic appears to be totally resistant. If your onions develop a severe infestation, grow your onions in an isolated plot, or spring plant all your onions. There is a predatory nematode (Neoplactana) available which is reported to give good biological control. If chemical control is used spray when leaves are 4 to 6" tall and later in the season if necessary.

Onion thrips

Thrips are most likely to cause damage during hot, dry weather. Humid, wet weather and frequent spraying with soapy water (2-3 tbsps/gallon) will reduce their numbers below damage level. Insecticidal soap is suitable for this purpose, but since thrips can be difficult to control it may be necessary to use a stronger insecticide such as an organic combination of rotenone, sabadilla, and pyrethrin.

Voles and field mice

Voles and field mice travel in the tunnels created by moles. As a preventative measure, moles should be discouraged, even though they do little direct damage. Since damage is most likely to occur in fall plantings, set out mouse traps (baited with peanut butter) in the fall. Continue trapping until you have trapped out most of the local rodent population. You may find it necessary to trap two to three times in the fall. This is one reason why it is best not to plant too early in the fall. Raised beds with wood frames may be protected from rodents by stretching hardware cloth or 1" chicken wire netting over the bottom of the frame before the bed is prepared. Rodents may also be controlled by vitamin D organic rodenticide or by Juicy Fruit gum rolled into balls and dropped into tunnels. In both cases the bait must be as free of human scent as possible.


Proper attention to crop rotation, growth conditions, harvesting, and curing techniques will greatly reduce the incidence of disease. The most likely and serious problem is onion neck-rot, which is encouraged by the following conditions: (1) late applications of fertilizer, especially nitrogen; (2) extended wet weather during harvest and initial stages of curing; (3) reduced air circulation around bulbs due to weeds or mulch applied too close to the necks of the bulbs; (4) presence of downy mildew due to extended rainy weather; (5) cutting off tops before the necks have completely dried. In general, strong-flavored varieties are more resistant than mild-flavored varieties of onion.


Smut is a common infection of onion seedlings that is most effectively controlled through crop rotation and using a fungicide seed treatment.

Downy Mildew and Purple Blotch

These are diseases that may be a problem during periods of high humidity. Fungonil Fungicide (50232) is an effective control.

Fusarium basal root rot

Fusarium basal root rot may cause serious crop losses but can be controlled by planting Fusarium-resistant varieties.

Neck rot

Neck rot is usually caused by Boytrytis fungus; however, it may be followed by a soft-rot bacteria. To control neck rot, plant varieties which mature properly so that neck tissues are dry before harvest.

Pink root

Pink root is caused by common soil fungi and can be prevented through crop rotation. Always follow the label instructions on any treatment products by consulting with local County Extension Services. Pink root (Pyrenochaeta terrestris) is one of the most common diseases. Caused by a soil-borne fungus, it induces root necrosis. Roots turn bright pink then die. Although new roots will form, infected plants may have only a fraction of the root system of healthy plants. The disease will reduce yields and bulb size because of an inadequate root system for the uptake of water and nutrients.

Fusarium basal

Fusarium basal rot is caused by a fungus, which can live in the soil for many years. It is a pathogen that enters the bulbs at the base through the root tips or through other areas which have been damaged by disease, such as pink root, insects or mechanical implements. Bulbs that have been infected may have visible basal rot. In some cases, bulbs may appear normal and firm at harvest but will begin to rot in storage. The outer scales of infected bulbs often have a subtle bronze or pink cast.

White rot, (Sclerotium cepivorum)

White rot, (Sclerotium cepivorum) is caused by soil-borne fungus whose pathogenic activity is induced by certain exudates from onion roots. The disease begins with a yellowing and wilting of the leaves, which will kill young plants. With later infections, the bulbs become soft and rotten, and can be easily pulled from the soil because the roots have died. A white mold develops on the bulbs. Because the fungus is specific to plants in the onion family and persists in the soil for many years, growing an alternative crop in badly infested fields is essential.

Botrytis neck rot (Botrytis allii)

Botrytis neck rot (Botrytis allii) is a common disease of bulbs in storage. The organism enters the bulb through the neck during the growing season or at harvest. The scales at the base of the neck collapse and become soft. A whitish-gray mold may appear on the fleshy scales under the dry outer scales. The bulbs gradually soften and the inner flesh appears frozen or cooked. Soft rot may set in and the bulbs could become smelly and rotten. To avoid Botrytis neck rot, foliar diseases should be controlled throughout the growing season, and onions should be harvested when they are mature and well cured.

Botrytis leaf blight (Botrytis squamosa)

Botrytis leaf blight (Botrytis squamosa), is a foliar disease that appears as small white spots surrounded by light green or yellow halos. The spots may expand to cover large portions of the leaves, which quickly turn yellow and die. Wet weather causes more leaf blighting.