What to look for 

Small black flies (2-3mm in length) with thinner bodies than fruit files.
If you're unlucky you may also see their larvae - they look like small white worms with black heads.

Why and how they turn up

You will get these almost anywhere there is soil that stays damp for more than a couple of weeks at a time. This makes them a perennial pest for isopod keepers.

Danger level

Whilst deeply annoying they are harmless to you and your isopods.

Prevention

Fine mesh over all ventilation holes

How to treat them

1 - Yellow sticky traps. Make sure if you use them in or near your enclosures there's no chance of your isopods making contact with them or them falling into the enclosure. Anything stuck to one of these isn't going to survive. Put them close to your enclosures and remember to change them once they've caught a goodly number.

2 - BTI.  Full name Bacillus thuringiensis israelensis. This strain of bacteria is harmless to everything apart from mosquito larvae and fungus gnat larvae (although we wouldn't advise eating a spoonful to prove this). The most common branded product is Mosquito Bits or Mosquito Dunks. However there are a range of other products that have this as the active ingredient. You can sprinkle powders/bits onto the surface of your substrate, mix it in, or make a 'tea' and strain out the solids and spray the liquid onto the substrate. This only affects the larvae so it won't immediately reduce the number of flies, and will likely need to be repeated every couple of weeks until the population dies out.

3 - Nematodes. Like with many pest species, there's a nematode that is a specific parasite for Fungus Gnats. Follow the instructions on the packet, but generally you either sprinkle the powder on or mix it with water and spray it on. These will only work on soil that is already damp, and should normally only need one treatment. Don't be too surprised if you have to repeat it a few weeks later though. If the larvae population drops low enough the nematodes will die off, but eggs laid towards the end of that will hatch out and there'll be nothing to stop the new crop of larvae.