Articles Fish disease

How to check aquarium fish for parasites

March 3, 2013

If you’re worried your fish has parasites or just want to make absolutely sure that new fish you have in your quarantine tank isn’t carrying any creepy things that could harm its future tankmates, your best bet is to check for parasites with a microscope. It doesn’t have to be an expensive, fancy microscope – I use a very old one and it works just fine.

If you don’t have a microscope but still really want to check your fish for parasites, ask around at school or work or try to find a friend that has one. You can ask the people you got the microscope from for help with it or check out this site I found for more info on how to use  it. Some vets and koi doctors will also check for you, but doing it yourself is easier than you think and will save some time and money.

When using a microscope to figure out whether your fish is carrying any creepy crawling things, you check either the poop (for internal parasites, also called endoparasites) or a skin scrape (for external parasites, also called ectoparasites) or both. You then take pictures of anything unusual you might find (keep reading for more info on that) to do a comparison search on the internet or to show to an expert.


I’ll tell you more about the poop and picture parts later; let’s discuss skin scrapes first!

Of course getting a skin scrape isn’t possible with most fish, which is not a disaster. If you have a specimen that’s big enough and won’t do strange stuff when it’s out of the water (I wouldn’t try it with a puffer, for example; they can try to puff and instead fill themselves with air, which is often fatal) it’s definitely worth a try. The skin scrape method is very popular in the fancy goldfish and koi world and a skin scrape from every new fish is examined under a microscope by all responsible dealers.

When dealing with smaller fish you can’t get a skin scrape from, like tetras, watching their behaviour could be enough. If you see them flashing (spazzing), breathing heavily or trying to scratch themselves, you might be dealing with an external parasite.

How to perform a skin scrape

Put the sample on the slide and cover it

Put the sample on the slide and cover it with the slip. This fish was big and quite stressed, so he had a thick slime coat; your sample may be smaller than this.

When you do a skin scrape, what you’re after is a piece of the slime coat of the fish, because that’s where the parasites will be in if there are any.

  • You’re going to need to lift your fish out of the water to do the scrape, so if you’re too scared it will get hurt or that you’ll do it wrong, take it to a vet or koi doctor. It’s quite easy to obtain a piece of slime coat, but I can imagine some people are just too scared they’ll drop the fish and want to see someone else do it first.
  • To perform the skin scrape, catch the fish and gently lift it out of the water. Most fish will wriggle and try to escape at first, but become calm after a few seconds.
  • Be sure to hold the fish firmly, but don’t squeeze it too hard or you may damage the slime coat.
  • You’re going to need either a spatula, the blunt side of a knife, or, if you’ve done this a few times before, a scalpel, to gently scrape from behind the gill cover to the tail, which should result in a nice blob of mucus.
  • Put the mucus on a clean microscope slide with a drop of aquarium water on it and voila! You have your skin scrape.
  • To examine it, put a cover slip on top of the sample, put the whole thing under the microscope and take a look. I usually work my way up from a 50x magnification to ~600x.

So now you know how to find ectoparasites, but there are plenty of parasites that live inside the fish (in the gastrointestinal tract for example) you might have missed this way. To find those, you take a piece of fresh poop (preferably a piece that hasn’t even hit the bottom of the tank yet) and examine it like you would examine the skin scrape – working your way up to a magnification of about 600x.

How to identify parasites

Don't worry if you find this in your sample! It's an innocent bubble of air. Picture taken with my phone!

Don’t worry if you find this in your sample. It’s an innocent bubble of air.

  • Seeing one or two parasites in a skin scrape or poop sample isn’t unusual, so don’t worry about that.
  • If you see many of them and aren’t sure what type they are, though, or if you encounter something suspicious you can’t really identify, it’s a good idea to open a topic on your favorite forum, do an internet search or ask an expert.
  • Some microscopes can take pictures and videos and transfer them directly to your computer, but to make identifying whatever you’ve found easier when you’re using a less fancy microscope, take a picture or make a video with your phone by holding the camera lens in front of the ocular lens just like you would hold your eye in front of it. You may have to wiggle the phone a bit before you get a clear view, but it should usually work just fine! This is a method that’s helped me many times.
  • If this doesn’t work for you, you can also try drawing whatever you see. Write down how many of these things you found, what the magnification is and how they move (if they move at all). That way you can ask others for help or try to find whatever is bugging your fish yourself.

Ew! These creepy things were found by Ute when she examined a fancy goldfish poop sample. They were causing the fish to become floaty, but now that they’ve been identified they can easily be wiped out with the correct medication.

And remember: don’t start medicating with the first medication you find without getting a proper diagnosis first. This can weaken the fish and eventually even kill it. Ask around on aquarium forums or mail a vet when you’re not sure what to do next. You can also contact me by leaving a comment. I can’t promise I’ll be able to help you, but I might be able to find people who can!

If you have any more questions about checking your fish for parasites and identifying whatever you find on them, don’t hesitate to leave a comment. Happy fishkeeping everyone!

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  • ReplyJohn crossJune 23, 2017 at 2:35 am

    Not sure if the last message went thru but here it goes one more time. I will be hlgetting together some samples and i would like you to look at them just to get a second opinion. It will be a fecal matter and slime coat sample. Should i take a sample from each fish pr just a few? Are you still activly keeping up on this thread?

    • ReplyMariJune 23, 2017 at 11:27 am

      Hello! I’m still here but I’m not sure if I’m the right person to help you out with this as I’m not an expert on fish disease. If I take samples myself I still always have to show them to more experienced people to help me figure out what i’m seeing! You could try the disease and diagnosis section of one of the various fish forums out there for a more reliable second opinion 🙂

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