Why Is My Greenhouse Full of Flies? How To Get Rid Of Them

You wouldn’t think this, but your greenhouse can become filled with all sorts of flies and other pests before you know it, and you might be wondering where they all came from. The fact is, there are two pests that seem to be the most prevalent in many greenhouses: aphids and whiteflies, so as you can see, flies and other pests are not nearly as rare as many greenhouse enthusiasts like to think.

We’ve put together the best guide on how to spot fly problems and more importantly, how to control and eliminate flies in your greenhouse.

Flies love the warm, usually dry, environment that they find inside greenhouses allowing them to bask in its heat. There is also usually a good source of organic food matter for them to feed on too!

Some pests will sneak inside of your greenhouse when the weather is too warm or too cold outside, but most pests make it indoors because they are brought in there unwittingly.

This includes pests that fly in once the door is open, land on your shoe or some tools, and then make it inside once you yourself go in, or they can even be hidden in brand-new plants that you’ve placed in your greenhouse then fly to other plants when no one is looking. In other words, not every fly or pest that makes it into your greenhouse is actually attracted to it. 

Indeed, many flies and pests come into greenhouses unknowingly, and it’s up to you to eventually find them and decide how to get rid of them. Fortunately, that is a lot easier than it might seem.

How Do I Keep Flies Out of My Greenhouse?

You’ll never be able to prevent all flies from getting into your greenhouse, but you can greatly reduce the number that does get in there with a few simple tricks. One of the simplest things to do is get some screens and place them in front of doors, windows, and any other openings you might have.

This can be detrimental, however, because it can affect the amount of sunlight getting to the plants. This is why many gardeners keep the screens across the openings only when windows and doors are open, then remove them once they are closed to maximize the effects of the sun on growing plants.

A small amount of flies in a greenhouse is acceptable. It’s only when they begin to swarm and constantly buzz around a gardener that they become a very unwelcome guest.

What Kinds of Flies Do You Get In a Greenhouse?

Surprisingly, there are several types of flies that love getting into greenhouses, and the most common types include:

  • Sap-feeding insects such as aphids, mealybugs, scale insects, mites, and whiteflies.
  • Pollen feeders such as thrips, fungus gnats, blow bottle (blue bottle) flies, and shore flies.

Aphids, mealybugs, and scale insects are very tiny and very slow, and they often secrete a sticky substance called honeydew.

Mites are nearly invisible insects and therefore you may need a magnifying glass to identify them, and whiteflies are not actual flies but instead are insects that look like tiny white moths.

Thrips look like tiny ants to most people and love to feed on flowers. Both fungus gnats and shore flies are tiny flies that love to feed on the roots of plants that have been overwatered.

Blow flies

How to Control Blow Flies In A Greenhouse

Blow fly, also called a blue bottle, is a blue-green fly that can carry diseases, which is why you never want them in your greenhouse. Blow flies breed when it’s warm and can hatch their eggs even sooner if the weather is too warm.

If you’re curious about how to tell if you have these flies, it is very simple. The adult flies will be seen hanging around decaying matter and on the greenhouse glass as well, so as soon as you see this, it’s time to take action.

You can get rid of blow flies in one of two ways. First, you can destroy the breeding source, which is usually some sort of decaying animal. Once you find the spot, you need to clean it thoroughly with a borax-and-water solution. Without getting rid of the breeding source, you’ll find it difficult to get rid of these flies in any timely manner.

Second, you need to get rid of all of the adult flies, and you can do this by hanging a yellow sticky fly catcher card, or a chemical spray.

After you know they’re gone, the best way to keep them away is to make sure no type of decay is ever inside or near the outside of your greenhouse, which is what they’re attracted to the most. Keep your greenhouse clean at all times, and you shouldn’t have any problems with these flies from then on.

Shore flies

What Are Shore Flies?

Shore fly
Taken by Martin Cooper. CC License

Shore flies are similar to fungal gnats except they have very short antennae. They have red eyes and dark heavy bodies, and because they are such good flyers, you can find them just about anywhere in your greenhouse.

Ironically, shore flies tend to only cause aesthetic rather than long term damage to a plant, so that isn’t something to be concerned about unless you are growing ornamental plants intended to be brought indoors.

Nevertheless, the adult shore flies can spread soil pathogens throughout the greenhouse, which of course is a big concern.

How To Spot Shore Fly Damage

The main part of a shore fly’s diet is fungi, so they are going to go wherever they can find this “food” source. Unlike fungus gnats, which will turn to healthy plants if there isn’t a decaying plant nearby, the shore fly will stick with the unhealthy plants most of the time.

Their feeding, however, can create wounds. Although they don’t usually bother the plant roots, they can cause a lot of damage to the leaves of the plant.

If you notice anything that looks like a “wound” on one of the leaves, or any other type of damage to the plants’ leaves, you might actually have a shore fly problem.

How To Control Shore Flies In A Greenhouse

So, how can you control your shore fly problem? There are certain common-sense measures, of course, because the main way to control these and any other pests is by practicing good sanitation throughout your greenhouse.

Also, if you notice any water or damp areas underneath the benches, get rid of it because any type of accumulation in those areas can attract these flies. A shore fly loves damp places that might allow them to find more fungi to eat!

Any type of moist potting soil that has a high organic matter content may contain either fungus gnats or shore flies, although this usually occurs when shore fly or fungus gnat larvae nestle into a moist spot and are brought into the greenhouse from another location, without you even knowing that you’ve brought in a problem.

Both shore flies and fungus gnats are notorious for “hiding” from greenhouse owners!

Yellow Fly CatcherEven potting mix and other debris should be removed from below benches because this is where a lot of pests breed. Proper grading and drainage can remove excess water and help you control gnat larvae, as can making sure you never have any type of decaying organic matter hanging around.

One of the smartest things you can do is thoroughly inspect any new plants coming into your greenhouse to make sure they haven’t carried any pests with them to their new home.

Hang a yellow sticky fly catcher card to keep an existing population under control.


What are Whiteflies?

Greenhouse whitefly
Taken by gbohne. CC License

As soon as you see a whitefly, you’ll know it because they are moth-like flies in a solid white color. They are similar to aphids in appearance but are much smaller.

There can be lots of them, but that doesn’t mean you can’t control them. Just look for their triangular, wedge-like shape and white color.

The one thing that whiteflies do best is making more of themselves, so once you find them it is very likely they’ll start reproducing in dangerous numbers. They can be difficult to control, but certainly not impossible.

How To Spot Whitefly Damage

One of the things whiteflies are best known for is their insatiable appetite. If you notice that any leaves of the plants in your greenhouse have a yellowish color or they’re starting to wilt, you might have a whitefly problem.

In fact, the whitefly eats so much that the plant leaves are usually the first thing to be sacrificed. In addition, the “honeydew” of the whitefly, which is essentially their feces, can attract diseases such as black sooty mold, which is another indication of their existence.

Whiteflies are spread on the surface of other plants. Therefore a greenhouse full of plants that have been grown from seed are less likely to be affected by greenhouse whitefly.

How To Control Whitefly In A Greenhouse

With such a voracious appetite, is there any way to truly control your whitefly population? Of course there is.

First of all, once you notice these flies on or near your plants, you can take your hose and wash them off of the plants. The blast of water should be enough to remove most of them.

The best method of controlling whitefly is to introduce a biological control called Encarsia formosa.

These are a tiny parasitic wasp that kills the whitefly. The eggs of these wasps can be purchased online. The timing of deploying this control is critical. The most effective time of introducing encarsia formosa is just as the first whiteflies are appearing.

You can also purchase an organic insecticidal soap, mix some in a spray bottle with water, and spray the plants thoroughly, especially the undersides of the leaves. If you need to, you can follow-up a few days later with another spraying.

You can also use a few of those yellow sticky cards that they sell at nurseries and other stores. But make sure that as soon as you see them, you take measures to eliminate them immediately because whiteflies can do lots of damage in just a short period of time.

Fungus Gnats

What Are Fungus Gnats?

Fungus Gnat
Taken by Andy Murray. CC License

The first thing you need to know is that fungus gnats love greenhouses, and in fact, both fungus gnats and fungus gnat larvae can be found in greenhouses of all types, sizes, and locations.

They are frustrating because the gnat larvae get comfortable in your growing medium then attach themselves to the plant roots, which means the plants don’t get the nutrients they need to survive. Hence, the plants die rather quickly. This means that if you’re going to eliminate these pests from your greenhouse, you have to get rid of them before they are actually found in the soil of your plants.

In other words, prevention is the best way to control these pests.

How To Spot Fungus Gnat Damage

So, how can you get rid of fungus gnats when they do most of their damage while you can’t even see them? Since the larvae of the fungus gnats are the biggest problem, trying to control them can be a challenge.

When you get new plants, do a thorough inspection of them, especially the leaves, and check for the larvae, which are usually whitish or yellowish in color.

Also, check to make sure there are absolutely no adult fungus gnats hanging around the plant. If either of these scenarios exists, quarantine the plants for two to three weeks until you get rid of any sign of fungus gnats or gnat larvae anywhere on the plants.

How To Control Fungus Gnats In A Greenhouse

Unlike short flies or whiteflies, fungus gnats like doing most of their damage underneath the soil, which can make it a challenge to control them properly.

As mentioned earlier, fungus gnats love greenhouses, but you can control them with a few simple measures. These include:

  • Do not over-water the plants. Try not to water them until the top two inches of the soil are dry and never sooner.
  • Use butterfly-shaped sticky stakes, which go underneath the plants and can get rid of some of the fungus gnat larvae that love to eat away at the plant roots.
  • You can also use a lot of mulch in your plants, because this will keep the fungus gnat adults away. Try a wood chip mulch, which is good for the plants and will deter the adults thanks to the material it is made of.

Trappify fly trapWhen you keep the fungus gnat adults away, no more eggs can be laid, so your problem should disappear quickly. In addition, keep in mind that the best way to control your fungus gnat problem is to prevent it from happening in the first place.

If you quarantine your new plants, you can not only get rid of existing problems but watch for new fungus gnat larvae and even adult flies.

Only when you are positive that you have no fungus gnat larvae or adult gnats should you include the new plants in the existing plant population.


Your greenhouse is there to grow beautiful fruits and vegetables, flowers, and herbs, but the first time you notice a short fly, fungus gnat, whitefly, or any other type of pest, it is time to take action immediately.

Trying to control these and other pests is mostly a matter of practicing good hygiene measures in your greenhouse, as well as doing something about it as soon as you notice a problem. 

Since so many pests are attracted to decaying objects, you should never keep any decaying organic matter anywhere in or around the greenhouse.

All greenhouses, regardless of what you’re growing there, should be cleaned regularly so that control of all pests is made much easier. If a problem with pests does occur, there are steps you can take to eliminate them and prevent them from returning in the future.

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