Onion storage diseases

Storage rots are caused by fungi and bacteria (Pseudomonas and Erwinia spp.) that live on organic matter and onion debris in the soil. These organisms are common in soil and will attack several different host plants. They become a major problem wherever onions are grown in a short rotation.

High field temperatures (greater than 30°C) favour bacterial decay, so these rots are more of a problem in warm climates.

Onions will store for up to 8 to 10 months provided they're:

  • treated correctly during and after harvest
  • prevented from sprouting.

Impact of growing conditions on storage rot

The growing conditions will also influence the quality of the onions in storage. For example:

  • Usually, onions grown slowly in cool temperate climates will store for longer periods than onions grown under irrigation in hot climates.
  • Extended periods of wet conditions in the 4 to 6 weeks before harvest will promote the storage rots caused by Aspergillus and Penicillium spp., especially in hot areas.

Other factors that will increase diseases in storage include:

  • high crop densities in the field
  • prolonged periods of wet conditions during crop maturity
  • damage due to pre-harvest diseases and pests
  • insufficient curing (field or artificial) at 27°C with a relative humidity of 80%
  • leaving mature crops in the field too long
  • rough handling during harvesting and grading
  • high temperature and humidity during storage.

Soil containing bacteria and fungal spores is washed or blown into the neck or base of onion plants during the growing phase of the crop and causes disease when conditions are suitable during storage.

General control for storage diseases

There are no fungicides registered for post-harvest treatment of onions.

Your general control measures should include the following:

  • use good crop hygiene, including proper crop rotations, sound growing practices and disposal of crop residues
  • turn onions frequently during field curing
  • avoid windrowing during periods of wet weather
  • handle bulbs carefully at harvest to minimise damage
  • keep bulbs continually dry after harvest
  • maintain good airflow and ventilation, low temperatures less than 20°C, and a low relative humidity during storage of less than 80 per cent.
  • forced air curing at 27°C and a relative humidity of less than 80% before storage will help minimise storage rots developing

Major storage diseases of onions

The major storage diseases of onions include:

  • bacterial rots
  • black mould
  • blue-green mould
  • fusarium rot
  • neck rot.

Storage disease

Causal organism


Bacterial rots

Pseudomonas and Erwinia spp.

Strong smelling watery rot of the bulb

Black mould

Aspergillus spp.

Sooty black masses under surface scales

Blue-green mould

Penicillium spp.

Dusty green masses under surface scales

Fusarium rot

Fusarium spp.

White fluffy growth and soft rot at base or neck of onion

Neck rot

Botrytis spp.

Dusty grey mould and rot in neck of bulb

Bacterial rots (slippery skin, sour skin)

Symptoms include a strong-smelling watery rot of the bulb. Bulbs might look sound but when cut open, the main scales are brown and water soaked. When pressure is applied, the inner core may be forced from the onion. Infected bulbs rot rapidly.

Black mould

Symptoms include sooty-black spore masses that usually develop underneath the surface scales and tend to be much more prominent than blue-green mould. Black mould occurs in a similar way to blue-green mould and often both occur together.

Black mould is caused by Aspergillus spp.

Hot weather in the field and during storage favours development and rapid spread of this disease. The ideal environment for black mould includes temperatures over 30°C with a relative high humidity.

Blue-green mould

Symptoms include green-dusty spore masses that develop along the mid ribs and under the surface scales when the weather is moist before harvest.

Blue-green mould is caused by Penicillium spp.

In storage the disease develops rapidly, especially in humid conditions when a sparse green, felt-like growth occurs in the neck, and on both surfaces of the outer scales.

Fusarium rot

Symptoms include a white fluffy growth and soft rot at the base or neck of the onion.

This disease is caused by Fusarium spp. It usually causes minor losses, but rotten onions in a bag can cause other onions to deteriorate.

In warm climates of 28°C to 32°C the rot normally starts in the field at the base of the onion and progresses into the bulb, causing a soft watery rot. This is often associated with bacterial decay.

Neck rot

Symptoms include:

  • a dusty-grey mass of spores that develops in the neck of the bulb
  • softening of the neck and occasionally black structures called sclerotia, up to 1.5cm diameter, form beneath the scales
  • a soft-brown rot develops and moves into the bulb.

The fungus causing the disease (Botrytis spp.) is carried on the seed. It remains inactive during the growing stages of the crop and generally there are no visible symptoms of neck rot until onions have been stored for 8 to 10 weeks.

Controlling neck rot

Seed treatment with registered fungicides is essential to control neck rot in storage. Check with the seed company that seed has been treated, particularly if the seed is from cooler regions.

Forced air drying at temperatures of 30°C will reduce disease but can also encourage the growth of black mould.

Neck rot and infection by Botrytis on other parts of the plant can occasionally occur in the fields when conditions are humid and wet.

Reporting an unusual plant pest or disease

Report any unusual plant pest or disease immediately using our online reporting system or by calling the Exotic Plant Pest Hotline on 1800 084 881. Early reporting increases the chance of effective control and eradication.

Please take multiple good quality photos of the pests or damage to include in your report where possible, as this is essential for rapid pest and disease diagnosis and response.

Your report will be responded to by an experienced staff member who may seek more information about the detection and explain next steps.

Report online


Schwarts HF, Mohan SK Edts. (1995) Compendium of Onion and Garlic Diseases. APS Press 54pp.

Page last updated: 07 Jul 2022