13 Common Allium Plant Pests and Diseases and How to Deal With Them

The allium family of plants has some of the most common and best-loved food crops in the world, with a variety of flavorful and healthy options like onions, chives, garlic, leeks, and scallions. But alliums can suffer from pests and diseases, just like anything else.

Alliums are usually easy to grow, simple to harvest, and trouble-free to store long term. But they can still have their problems. They’re not immune to issues like dampening off, cutworms, aphids, downy mildew, and thrips.

That’s why it helps to know what you’re facing and how to deal with it.

Common Allium Pests

Whether you’re growing scallions, spring onions, hard-necked garlic, leeks, or soft-necked garlic, alliums all have similar needs. Plant them in well-drained, fertile soil with plenty of sunlight. Both onions and garlic prefer soil with an ideal pH – 6.5 or 7.0 is perfect.

Giving them the right condition goes a long way toward keeping your alliums healthy.

Like any plant with generations of cultivation behind it, alliums have a number of pests to contend with, and they can share pests easily, though some that harass onions will leave garlic alone.

If you’ve had trouble with pests, crop rotation is a good preventative practice. Move your alliums each season to confuse the pests that have overwintered in last season’s onion bed.

Garlic has very few pests (though it shares many of the diseases common to onions). Onions have a few very damaging pests as well. Chives, scallions, ornamental alliums, leeks, and shallots, on the other hand, tend to have more.

1. Allium Leafminer

This pest is new to North American allium growers. It became a noticeable problem only recently, in 2016. But allium leafminer (Phytomyza gymnostoma) is already a devastating pest.

These tiny insects can devastate your garlic, onion, leek, and other allium crops. Tiny, cream-colored grubs leave a trail of wavy, shrunken, and damaged leaves behind them as they feed.

Allium leafminers spend their larval stage on the allium plant, then drop off to pupate in the soil. The adults emerge as flies and quickly lay eggs on nearby allium plants.

Controlling these pests is simply a matter of crop rotation and row covers. Move your alliums each spring and cover the young plants with row covers to prevent adult allium leafminers from laying eggs on your alliums.

2. Onion Maggots

Onion flies (Delia antiqua) are a common pest of alliums. It’s the larvae that do all the damage. These hideous, quarter-inch long white maggots feed on roots. They can easily kill seedlings and older plants.

But they often burrow into bulbs, feeding slowly. Affected bulbs are absolutely inedible. Destroy any infected plants. Don’t compost them – onion maggots can thrive in compost piles.

Crop rotation and beneficial nematodes are great ways to prevent infection. Try applying nematodes to the soil before planting your onions. Then, cover young plants with row covers to keep the adult onion maggot fly from laying eggs on your plants.

3. Lesser Bulb Flies

Lesser bulb flies (Eumerus) are only “lesser” in relation to onion maggots. They cause similar damage to onions (and occasionally garlic), but rarely on as large a scale. Lesser bulb fly larvae are about twice the size of onion maggots and yellowish-grey in color.

Treat them as you would onion maggots, with beneficial nematodes and row covers. Destroy affected plants.

With both onion maggots and lesser flies, it’s important to clear every onion out of the garden at the end of the season. Without onions to feed on, these flies will die. So avoid leaving an allium or two to rot in the field – it’s an invitation to onion maggots and lesser bulb flies.

4. Wireworms

Wireworms are slender, tough-bodied little worms that are the larvae of click beetles in the Elateridae family. They rarely grow above one-and-a-half inches long and they feed on roots and bulbs. You’ll notice the tops of your onions growing yellowish and wilted as the roots are slowly destroyed.

Fortunately, wireworms can be managed with nematodes as well. The treatment for onion maggots and bulb flies works just as well on wireworms.

Common Allium Diseases

Alliums can fall prey to a wide variety of diseases. Despite the fact that alliums themselves are anti-viral, anti-biotic, and anti-fungal in their effect on humans and animals, they’re not immune to a variety of garden viruses, bacteria, and fungi.

Don’t make the mistake of trusting your alliums to stand strong against all the pathogens that have developed specifically to attack them. Fungi are the most common cause of allium issues.

While many allium diseases refer specifically to onions, these pathogens can just as easily attack garlic, leeks, and other allium cultivars as well.

5. Pink Root

If the bulbs and roots of the plant are pinkish, while the tops are stunted and yellowish, the plant has pink root. This fungal disease (Phoma terrestris) causes the roots of the allium to shrivel and die. Once the disease has set in, there’s no cure. Destroy affected plants completely.

To prevent pink root, make sure to space your alliums well. Plant them in well-drained soil. You can apply a copper-based fungicide as a preventative measure if you’re concerned about pink root.

It may reduce the spread of pink root or prevent a resurgence of the disease. But, if you’ve had problems with pink root before, the best option is to plant resistant cultivars such as ‘Early White Supreme,’ ‘Tokyo Long White,’ or ‘Super Star.’

6. Fusarium Bulb Rot

Bulb rot is a fungal disease (Fusarium oxysporum) that affects the bulb and stem of alliums. Unfortunately, no cultivars are fully resistant to Fusarium bulb rot, though you can reduce the chance of this disease by planting semi-resistant onion varieties like ‘Early Yellow Globe’ or ‘Pulsar.’

Alliums affected by Fusarium bulb rot have soft, weak necks. The bulbs become soft, brown, and rotted. Eventually, the entire plant rots away. Destroy affected plants immediately and treat the rest of your alliums with a copper-based fungicide to reduce spread.

7. Onion Yellow Dwarf Virus

This virus starts by causing yellow streaks and crinkled leaves on the stalks of alliums. The flower stalks are often yellow and twisted, producing few seeds. The bulbs of alliums affected by Yellow Dwarf Virus are undersized.

Yellow Dwarf Virus is commonly spread by aphids. To control the spread of this disease it’s essential to do what you can to prevent aphids.

Spray your allium beds with insecticidal soap if you notice aphids in your garden. Or, use neem oil to break up their life cycle. Row covers and trap crops can help, as well.

8. Neck (or Bulb) Rot

Too much water right before harvest can cause a devastating bacterial issue, neck rot. It’s caused by the bacterium Pseudomonas viridiflava.

The necks of allium bulbs rot and gray mold develops right inside the bulb. Neck rot is more common in damaged bulbs because the damaged point gives an area of entry for the bacterium.

Destroy all infected bulbs when you see them in order to reduce the spread. Cut way back on watering right before harvesting as well. Mature alliums don’t need as much water as young ones.

You should also cure bulbs properly before storing them to reduce the chances of rot developing in storage.

9. Smut

Of all the allium diseases, this one is a real problem. Smut leaves young alliums with black-streaked stalks filled with a soft, dark brown powder. It’s caused by the fungus Urocystis colchiciand cool soil produces the ideal environment for allium smuts to thrive.

If your soil feels too cool for comfort, warm it up by covering it in clear plastic for a few weeks before planting. Not only will this warm the soil, but it may also solarize it – killing off a wide range of pathogens.

There are two onion cultivars that are highly resistant to smut. ‘Evergreen Hardy White’ and ‘Tokyo Long White’ are great options for areas where smut is a constant concern – such as locations with cool spring and early summer temperatures.

10. Onion Smudge

Alliums with onion smudge develop bulbs with dark green or black, ringed spots. Onion smudge is caused by the same fungus that causes anthracnose in other garden crops. Onion smudge usually appears right before harvest or even in storage.

Destroy all infected bulbs. Fortunately, both yellow and red onions, as well as most garlic, are resistant to onion smudge. All white onions are at risk, however, so store them separately and stick to resistant varieties if you’ve had trouble with smudge in the past.

11. Purple Blotch

This fungal disease (Alternatia porri) causes the leaves of alliums to develop sunken, light-colored spots with concentrically ringed, purple centers. Gradually the spots enlarge and girdle the leaves, causing them to wither and fall off.

Like so many fungal diseases, purple blotch spreads best in cool soil. Cover the ground with clear plastic for a few weeks to warm it up before planting.

If you notice purple blotch forming on your alliums, treat it with a sulfur or copper-based fungicide to prevent spreading.

12. Rust

Alliums with rust (Puccinia leeks) develop small, reddish-orange blisters on their leaves. Eventually, leaves with rust symptoms turn yellow and die off. The bulbs of rust-infested alliums are undersized. Allium rust can also infest asparagus plants so keep these two crops separate.

To treat rust, use a copper-based fungicide and keep your garden clean. Dispose of all discarded alliums and allium tops. This will make it impossible for spores to over-winter in the garden. If you have a rust outbreak, rotate your crops and solarize the soil before the next growing season begins.

13. White Rot

White rot is a fungal disease caused by the fungus Stromatinia cepivora. When it’s present, it causes the leaves to turn yellow before wilting and dying back. Underground, the root is rotting away and is covered in a white fungus.

Crop rotation is key to avoiding it and you can treat with regular applications of copper fungicide, though once the bulb starts to rot, it’s too late to save it.