Koi Skin Scrapes: A How-To Guide

Skin scrapes are vital to accurately diagnose fish parasites. This photo illustrates the proper technique for performing a skin scrape.
Skin scrapes are vital to accurately diagnose fish parasites. This photo illustrates the proper technique for performing a skin scrape.

If your koi are behaving oddly,
you’ll need to determine the reason for
the strange conduct in order to resolve
the issue that has occurred. First, analyze
pond or tank water with a test kit to
determine if all water parameters are
within acceptable levels. Simple tests can
rule out water quality as the trigger for
unusual koi behavior and point you in a
different direction. If water quality passes
with flying colors, then proceed to parasite
activity as the next possible cause.

Fish Parasites

Fish parasites are both microscopic
and macroscopic. Skin scrapes must be
performed to identify microscopic parasites,
as this type cannot be seen with
the naked eye. Fish parasites are usually
discovered this way; the majority of
harmful koi parasites are microscopic.
(Fish are like dogs and cats in that if you
don’t actively prevent parasites, you will
end up treating for parasites.)

The purpose of taking a skin scrape is
to obtain a sample of mucus from a koi’s
cuticle, or slime coat, for analysis under
a microscope. The mucus specimen is
examined for significant parasitic existence.

Remember that parasites are always
present in low numbers, but when a koi
has been stressed the parasites will flourish
and can become problematic.

Typical koi behavior suggesting that
skin scrapes should be performed:

  • Flashing and darting, or rubbing on
    pond edges, as if to rid an irritant
  • Loss of appetite and general
  • Hanging motionless in water
  • Unusual gill activity; clamped gills
    or excessive movement or panting
  • Clamped fins
  • Isolation; not mixing with other koi
  • A foggy eye, patches of fungus,
    bumps, sores, ulcers or lesions on the
    body or fins
  • Congregating in high oxygen
    concentration areas such as waterfalls or
    around air stones
  • Lying on its side on pond bottom,
    exhibiting sharp movements if disturbed
    only to resume lying-down position
  • Reddening of skin or fins
    Performing skins
    scrapes can be a daunting
    task. Getting
    good quality skin
    scrapes will take practice.
    Accurate parasite
    identification with a
    microscope will take
    even more practice.
    With time, you’ll gain
    confidence in handling
    your koi and become
    proficient at obtaining
    and preparing specimens
    for microscopic
    examination or biopsy.
  • Prep Work

    Things you will
    need to perform
    successful skin scrapes:

  • Sock net
  • Koi viewing bowl
  • Sterile glass slides
  • Sterile plastic cover slips
  • Microscope
  • Pen and paper
  • One cup of pond water
  • Eye-dropper
  • Tweezers
  • Hand towel
  • A helper
  • Assemble all necessary equipment for proper and successful skin scrapes or gill biopsy before netting your koi.
    Assemble all necessary equipment for proper and successful skin scrapes or gill biopsy before netting your koi.

    Assemble all of the necessary equipment
    on a clean, dry surface. Before you
    begin, decide how many scrapes you will
    be performing. Set out a clean piece of
    paper for every scrape, and label and
    number each one with a corresponding
    scrape location: left flank, flank to
    tail, right gill, et cetera. These sheets of
    paper will keep your slides organized
    and provide a great place to jot down
    notes both during sample collection and
    during examination with a microscope.

    See the sidebar for a list of suggested
    skin scrape sites. Once you’ve made these
    preparations and have chosen your sites,
    you’re ready to begin!

    Performing Skin Scrapes

    Fill a koi viewing bowl with water
    from the tank or pond just to a depth
    sufficient to cover the fish. Using a
    sock net, carefully put one koi into the
    viewing bowl. You will be holding the
    fish with one hand and performing the
    skin scrape with the other. Try not to
    touch the areas designated as scrape
    sites. Never blot, wipe or wrap the koi
    in a towel. This would remove the pests
    that you are trying to capture from the

    When handling koi you should try
    to remain calm and maintain quiet
    surroundings. If the koi is of substantial
    size, a helper may be needed. It is a
    good idea to give your koi a break and
    a chance to breathe in between each
    scrape. By releasing it momentarily,
    you’ll ensure it gets through the ordeal
    with minimal stress.

    Start by holding your fish against the
    side of the viewing bowl with its flank
    (side) out of the water. Grasping the
    slide firmly, hold it at a 45-degree angle
    and press it down on the fish. Apply
    some pressure and drag the edge of the
    slide along the flank, from the shoulder
    toward the tail. Never go against the
    scales, as damage may occur. By applying
    slight pressure you should be able to
    scrape some mucus from the skin. You
    only need a small amount; about the size
    of a pencil eraser. The intended prize,
    mucus, will be clear or vaguely opaque.

    Once you have a
    sample on the slide,
    place one drop of
    pond water on top
    of the mucus and
    gently place a cover
    slip on top of the
    mixture. The cover
    slip will force the
    mucus to spread out
    on the slide, perfect
    for viewing under a
    microscope. Place
    your prepared slide
    on the appropriately
    labeled paper and
    keep it out of direct
    sunlight. Now, move
    on to gather more

    Obtaining a sample of gill tissue is challenging but crucial for properly diagnosing gill parasites and/or gill disease.
    Obtaining a sample of gill tissue is challenging but crucial for properly diagnosing gill parasites and/or gill disease.

    For best results,
    your samples should
    be examined within
    30 to 60 minutes of being collected.
    Tweezers will come in handy if any
    macroscopic parasites are discovered,
    such as anchor worm or fish lice.

    Gill Biopsy

    Taking a sample from the gill of
    your koi is a little trickier. Fish really do
    not like to cooperate with whomever is
    lifting their gill plate cover (operculum)
    or sticking an object under it. You will
    most likely need a second set of hands to
    help when taking gill samples.

    Now is your chance to get a good look
    at the gills and visually inspect them for
    damage or signs of tissue malfunction.

    You should take note of
    anything unusual, such
    as pale pink streaks or
    areas of discoloration
    within the normally
    crimson red gill tissue.
    White edges, frayed
    tips, holes, heavy mucus
    or blood clots on the
    gill filaments are also
    reasons for concern.
    Also, any buildup of
    scar tissue resulting in a
    trunk-like appearance of
    the individual delicate
    gill tissues is an indication
    of heavy parasite
    infestation. All of these
    conditions are evidence
    of gill damage from
    parasite activity or may
    also be an indication of
    chemical burn.

    Instead of obtaining
    a mucus sample with
    the edge of a glass slide,
    this time you will use
    a sterile plastic cover
    slip to retrieve the gill

    Performing Gill Scrapes

    Again, hold your fish
    against the side of the
    viewing bowl. Working
    quickly, lift the operculum
    and gently wipe
    the gill filament with a
    corner of the cover slip,
    then release the fish.
    This sample will look
    different than a body
    skin scrape. It will be
    pink or red and look
    like tissue rather than
    clear mucus. Don’t be alarmed if you get a little bit of blood with the sample or
    if the fish bleeds from the gill following
    the procedure. Place the cover slip,
    sample side down, on a clean glass slide.
    To stay organized, set the slide down
    on your previously numbered sheet of
    paper. Now you can study the scrapes
    under a microscope and review your
    notes, or continue taking more samples.

    Happy, Healthy Fish

    Performing a skin biopsy or skin
    scrape can be intimidating, and getting
    good quality scrapes will take practice
    and patience. But if your koi are not
    their usual, lively selves, getting quality skin scrapes — and learning to analyze
    them — is the first step in restoring
    them to health! The sooner you accurately
    diagnose the existence and type
    of parasites that may be plaguing your
    koi, the sooner your fish will be bright,
    active, happy and healthy again.

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