Taking a skin scrape and gill biopsy from a big fish

In this article we will tell and show you, step by step, how to perform a skin scraping and gill biopsy on large aquarium or pond fish. Sometimes it is necessary to examine the skin and gills of fish for microscopic parasites. For pond fish or large aquarium fish, we can perform a skin scraping and gill biopsy using a slide to create a sample for microscopic examination.

What you need

To perform a skin scrape, we need the following tools and objects:

  • Two buckets or containers with lids to temporarily hold the fish – one for sedation and one for recovery
  • Fish net
  • Standard sized microscope slides
  • Cover glasses
  • A pipette or syringe
  • Gloves
  • Tweezers
  • Paper tissues
  • A well-lit workstation


Before we can take a skin scrape or gill biopsy, we need to do some preparation. First of all, find a bucket or container suitable for the size of the fish you want to take a scrape from and label it, so you know what bucket you need to put the fish in. We will call it ‘recovery’, since we will be putting the fish in it after the scrape and biopsy. Rinse the recovery bucket with water and fill it with enough water to cover the fish. Get a second bucket, which will be used for the sedative, in case you want to use it (also label it). Later in this article we will also cover methods without using a sedative. Also rinse the sedation bucket with water and fill it with enough water to cover the fish. Use a convenient amount of water for sedation, such as 5 liters. Add the sedative and stir properly to dissolve, following the product instructions.

Doing the scraping and biopsy

Now that we have prepared the buckets we can move on. First, catch the fish with a net and place it in the prepared sedation bucket. The fish may be agitated for the first few minutes, so cover the bucket with a lid to prevent the fish from jumping out. Don’t rush it and wait until the fish is calm before performing the skin scrape, as it will be easier to handle the fish.

When the fish is calm, carefully lift it out of the water and position it so that you can scrape in the direction from head to tail. If the fish is not calm enough, return it to the sedative for a bit longer. Hold the slide at a 45-degree angle and gently, without pressing hard, scrape along the lateral line and then along the base of the dorsal fin. If you use the same pressure as when writing with a pencil, you will not hurt the fish. A sample of slime and perhaps a few scales will be left on the glass.

Carefully set this slide aside and take a new slide for the gill biopsy if you also want to examine the gills. Hold the fish in one hand and carefully open the gill cover with your finger or with your other hand. Insert the slide into the gill area, holding it parallel to the gill cover. Then, carefully, scoop out a small sample by scraping over the gill tissue. You may see a little bit of blood in the sample, which is normal because the blood vessels are on the surface of the gills and may be slightly damaged. Don’t worry, this bleeding stops quickly and the fish will recover rapidly from this small injury. To regain consciousness, release the fish into the recovery bucket with aquarium or pond water and put a lid on it. The scraping part is done!

Now let’s move to the microscope. Using a cover glass, move the sample you took to the middle of the slide. If there is not enough liquid, use a pipette to put a drop of water onto the middle of the slide and lower the cover glass. Press gently with the tweezers to distribute the smear between the cover glass and the slide. The specimen is now ready for microscopic examination. It is important to examine the slides within five minutes after the scraping because we are trying to find parasites that move, and some parasites will stop moving after about 5 minutes.

Alternative method for taking a skin scrape (without sedation)

If you prefer, you can also place the fish on a wet towel instead of holding it in your hand during the procedure. To do this, simply soak a towel in pond or aquarium water and place it on a flat surface, such as a table. If sedation is not available, you can use the wet towel to calm and restrain the fish while performing the skin scraping. It’s important to note that a gill biopsy should not be done without a sedative.

Another way to perform a skin scrape without sedation is to keep the fish in a container and wait until it calms down. Position the fish from left to right and gently cover its eyes and head with your left hand. Lean the fish against the container wall with both hands and lift it partly out of the water. Make sure there is not too much water in the container. With your right hand, make the scrape.

Final notes

Remember to always follow proper procedures and use the necessary tools to keep the fish safe during the examination. In an upcoming article and video, we will discuss the different types of parasites that can be found on fish and how you can identify them.

If you have any questions or comments, please leave them in the comment section below and we will be happy to answer them. Don’t forget to like and subscribe to our YouTube channel for more informative videos on fish health and care.

Good luck! If you have any questions, don’t hesitate to contact us.


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