How to Treat Koi Gill Flukes (Fish Safe Treatments)

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Guide to Treating and Preventing Koi Flukes 2022 (Best Fluke Treatments)

How to treat koi gill flukes
Flukes can infect both the body and gills of koi and can display signs of irritation as they grow and spread. Public domain.

A common type of freshwater parasite that can infect all types of pond fish are called flukes, which include skin flukes and gill flukes. Both types of fluke are visually similar, with both species attaching themselves to the body of the fish to feed on upper layers of skin and gill tissue. Koi can become infected with both types of flukes at the same time, but it is more common for just a single type to start causing problems unless water conditions are particularly bad.

Since flukes are microscopic, the only way to determine if your koi are infected is to take a skin/gill scrap and check under a microscope, or to try to identify common behavioural and appearance changes caused by the parasites. Like many other types of parasites, flukes are specific to different types of fish, and koi will have their own particular fluke that specializes in carp. Flukes can attach themselves to other fish for a short time, but they would eventually need to find the correct host to survive and breed. Luckily, flukes are more of a nuisance to koi in the early stages and should not cause any long-term problems with health if treated quickly. Flukes by themselves will cause irritation to fish, and will gradually stress the koi leading to them eating less and acting strangely. As the number of flukes grow, koi will become weaker and the flukes will start spreading to other fish, so it’s always good to treat any possible fluke outbreak early to stop the problem in its tracks!

Different Types of Fluke Parasites (Comparison)

1) Gill Flukes (Dactylogyrus)

gill fluke under microscope
A gill fluke under a microscope showing (a) “dark spots” on head and (b) the opisthaptor on the tail for attaching to its host. Public domain.

Gill flukes are the type of fluke you more commonly hear about, as they’re easier to identify in both visual appearance and symptoms. They’re larger than skin flukes, measuring up to 3mm in length, but you will still need a microscope to properly identify them as they’re transparent and still too small for the naked eye. Gill flukes have a slender cylinder body shape, with dark spots on the head of the body which skin flukes do not have. They also have a set of hooks known as an “opisthaptor”, which is a specialized organ for attaching itself to the tissue of fish. Both flukes have these hooks which are similar in shape, so the easiest way to identify the difference under a microscope is the dark spots present on the gill fluke.

Also, unlike skin flukes, as their name suggests, gill flukes attach themselves primarily to the gill tissue of fish rather than the body. Within the gill, they feed off mucus excretions and tissue and can cause open wounds, ulcers, and even infection from bacteria and fungus if they’re left untreated.

Common gill fluke symptoms include:

2) Skin Flukes (Gyrodactylus)

Gyrodactylus skin fluke under microscope
A Gyrodactylus skin fluke under a microscope. Source: The Scottish Government – Gyrodactylus Salaris Working Group (GSWG)(Archive), via Wikimedia Commons

Just like gill flukes, skins flukes attach themselves to koi and feed from the upper layers of tissue and membrane. Skin flukes, however, do not attach themselves within the gills but instead will feed on the outer body of the fish, so can be found anywhere on the outer scales.  Skin flukes are smaller than gill flukes, around 0.4mm in length but can still be seen under a microscope after performing a skin scape of the fish. Visually, they lack the dark spots present in gill flukes but have a similar cylinder-shaped body and hooked opisthaptor on the tail for attaching to the host.

Skin flukes breed without laying eggs, and give birth to live larvae, making new flukes immediately able to search for a new host fish. They show similar symptoms in koi, and should be treated the same as gill flukes before they can spread.

Common skin fluke symptoms include:

  • Rubbing against pond liner/objects
  • Irritated skin or ulcers forming (wounds)
  • Dulling in color
  • Hiding/shyness
  • Koi not taking food

Flukes Under Microscope – What Do They Look Like?

Since flukes and most other freshwater parasites are microscopic, the only way to “see” them and confirm they’re the problem is with a scientific microscope. You can check out our guide to the best microscopes for assessing aquatic microorganisms in your pond here. You would need to take skin or gill scrapes from your koi and then check the samples under the magnifying lens. This would allow you to see both gill and skin flukes, but as it requires the use of professional equipment, it may not be an option for everyone. What do they look like under a microscope? The below video shows an aquatic fluke under 400x magnification using a professional microscope:

If you don’t want to invest in a microscope to identify your potential parasite problem, you would simply need to look for signs of parasites from the behaviour and appearance your fish take. Changes in color, pattern, and behaviour are all signs that could point to parasites, with a precautionary treatment being advised to be on the safe side!

Where Do Koi Fluke Parasites Come From? 

where do gill flukes come from?
Flukes and other parasites are often brought to a pond by other animals, such as ducks and herons. Public domain.

Flukes, just like any other parasite, could have always been present in your pond, but it’s more likely they were brought to your system by visiting animals and wildlife. Both predators and pests can bring all sorts of harmful bacteria, fungi, and parasites to a fish pond unless you implement deterrents. Herons which are hunting fish and ducks who visit the pond are two of the worst culprits, with both being capable of spreading a wide range of diseases and parasites. The flukes may have been brought by the feathers of the bird, or the eggs may have been present in the faeces (waste) of the animal. Preventing predators and ducks from entering your koi pond will help stop parasites and bacteria from spreading, and will also help with both stress and water quality.

Another common way flukes may get into your water is when you introduce new fish or plants to the pond. It’s almost impossible to tell if a young fish has symptoms of parasites, and even with a skin scape, you may not catch any hiding eggs or larvae. The same with plants, it’s very difficult to know what exactly is attached to the plant until it enters your pond and starts to spread and cause problems. In many cases, this is just a risk you have to take as a fish keeper, but so long as you understand the signs and symptoms of problems and act accordingly, everything can easily be treated.

Gill flukes can survive winter
Flukes won’t be active in cold weather but they can hibernate and cause infections when warm weather arrives. Public domain.

Can flukes survive in very cold water?

One of the most common times for koi to get flukes is during torpor in winter, as their immune systems have slowed down to a crawl, making them more vulnerable. Flukes can survive in both very warm and cold pond water, with the only change being their offspring’s incubation (hatching) period. Eggs laid by gill flukes will hatch within 4 days in the water around 20°c (summer), but can take 5-6 months to hatch in the water around 1-3°c (winter). This means flukes that infect koi in winter lay their eggs and remain dormant throughout the season, and then start to hatch in huge numbers in spring. Even if the flukes themselves die off, their eggs will remain and start to spread when water temperatures rise.

For this very reason it is good practice for koi keepers to treat their pond water for both bacterial infections and parasites just before Winter and then again at the start of Spring. This ensures koi are not infected during their winter torpor, and provides the safest kick-start to the new year when Spring arrives. Correctly “winterizing” a fish pond is recommended for all pond owners with koi.

Should my koi be quarantined from other fish?

A koi with very advanced flukes can be quarantined for additional treatment if the fish is also suffering from open wounds or ulcers. In these cases, koi would benefit from being placed in a closely monitored holding tank and treated for both bacterial infection and parasites at once. This will reduce stress on the fish and give you more control over water conditions and treatment dosing.

For the early stages of flukes, fish do not need to be quarantined, with it being easier to just treat the pond as a whole to be on the safe side. Even if you perform skin scrapes of all koi and only find flukes on a single fish, this does not mean you don’t have free-swimming larvae or eggs elsewhere in your water. It is also very easy to miss flukes, as they’re absolutely tiny, so quarantining is often unnecessary and only helpful for treating koi with more advanced symptoms. If your fish are showing signs of flukes, or you’ve identified a single fluke, we recommend performing a full treatment and then adding preventive measures to help protect against flukes in the future.

Koi Fluke Medicine & Treatment Options (Best Fluke Products)

Note:  Always read dosage instructions before treatment, and make sure to turn off any UV clarifiers and remove any carbon filtration as it will neutralize medications. 

Treatments for flukes and most other common parasites include things like praziquantel, malachite green & formalin, potassium permanganate, or superverm. These are all chemical-based treatments with varying degrees of safety, but all can be effective when dosed correctly. Salt is also a natural and effective remedy against flukes, but would require the fish to be individually bathed to work, and would also not be able to treat any free-swimming flukes or eggs in the water.

We personally recommend either a praziquantel based treatment or a malachite green & formalin treatment but would lean more towards the former due to its superior results against flukes in particular. Both are wide-spectrum parasite treatments, being able to combat both kinds of flukes and various other diseases in freshwater fish.

aqua prazi treats gill flukes

Option 1: Aqua Prazi (Recommended)

Aqua Meds Aqua Prazi is one of the best fluke treatments available, and will quickly work to destroy both gill flukes and skin flukes in fish. It is safe for koi, goldfish, and biological filter media, and should have minimal negative effects on the eco-system when dosed properly. The medicine contains praziquantel and is primarily designed to kill flukes, but will also work on tapeworms and anchor worms. In terms of dosage, a single dose (10g per 100 gallons) added to the pond will kill all adult flukes within 24 hours of treatment. Afterward, a second follow-up dose is required 3-7 days later to kill any hatching larvae. The full treatment cycle will therefore be 1-2 weeks for total parasite removal. A 25% water change before each dose is recommended for maximum results.

Option 2: EcoLab Disease Treatment (Alternative)

natural gill fluke treatment

An alternative is Eco Labs Broad Spectrum Disease Treatment, which contains both malachite green and formalin. Even though this medicine is not directed at flukes in particular, we know from experience it can still be very effective. It will be able to kill a wide range of parasites, including flukes, and also treats a range of diseases, such as costia and fungal infections. The treatment is added to the water the same as Aqua Prazi, and can be repeated if necessary.

If your fish is showing signs of injury or has open wounds due to parasites, treatment with a wide-range antibacterial is also recommended to reduce the risk of infection and to allow better healing. We recommend API Pond MelaFix which is great for bacterial infections, damaged gills, ulcers, and open wounds in koi.

Tips for Preventing Koi Flukes from Infecting Ponds

1) Stop Animals Visiting (Predators/Pests)

Since most parasites are brought into a pond by other animals, one of the best ways to guard against flukes is to prevent animals from entering your water in the first place. Ducks and herons, in particular, can bring all sorts of parasites and diseases to a pond and both can be dangerous to fish. Herons will actively hunt your fish, causing stress and injury, whereas ducks contribute to sludge, ammonia, and problems with water quality. Both predators and pests can be easily deterred with a bit of preparation and investment, and we would strongly recommend it for koi as they do not react well to changes in environment and water conditions.

  • For more information on deterring herons, check here.
  • For our guide on stopping ducks from coming to your pond, see our article here.

2) Improve Water Conditions

Flukes and other parasites thrive in low-quality water conditions, and in these same conditions, koi and other fish will become more vulnerable. A pond with bad quality water is more likely to house harmful bacteria, fungi, and parasites in comparison to a well-filtered pond with low ammonia and waste. Keeping water in top quality condition is a main goal in fish keeping, and not only will this prevent parasites from spreading, it also ensures koi are in good health to fight back any problems if they occur.

Maintaining good water quality includes optimizing filtration, cleaning filter media, testing water quality, cleaning out excess waste, and providing plenty of aeration. For further reading, check our dedicated articles below:

3) Keep Koi In Optimal Health

Keeping your koi fit and healthy ensures they’re in a good position to fight back any problems that may occur in their environment. One of the best ways you can do that is to ensure you’re feeding your fish top-quality food with the correct nutritional profile. Many “budget” koi foods contain too much of things koi don’t need, and not enough of things they do. For example, cheaper foods will have far too little protein content, and the sources of protein may be from low-quality sources to save money. Most cheaper foods also contain no vitamins, minerals, or essential oils which koi need to maintain healthy slime coats and strong immune systems.  Picking a top-quality feed is vital to healthy koi, and will help them remain strong throughout their adult life.

4) Prepare Pond for Winter

Koi are more susceptible to both harmful bacteria and parasites during torpor/hibernation in winter, as their immune system has slowed along with every other bodily function. Making sure koi are well fed in summer, and correctly “winterizing” your pond will ensure they have the best hibernation period possible and the best kick-start to spring.

29 thoughts on “How to Treat Koi Gill Flukes (Fish Safe Treatments)”

    • Hey Brian,

      Praziquantel (Aqua Prazi) should work immediately on contact with the parasite, killing the adult flukes outright. No treatment can kill eggs, however, so you would need to always perform a repeat dose to destroy hatching larvae – 3-7 days later.

      Personally, I’ve had good results with a single dose (10g per 1000 gallons) over a week period, which I then repeat the following week. If you have a particularly bad infestation, dosing the second treatment 3-4 days after the first is also fine and should get to work faster. Total parasite removal will therefore take around 1-2 weeks total, depending on your treatment frequency.

      • Where do you buy the liquid stuff because i can only find powder on amazon- I need this fast have a 7,000 gallon pond i need to treat.

        • Hi CC,

          Unfortunately I’ve only ever used powdered praziquantel, so I’m unsure exactly where to find liquid products for ponds. Could I ask why you want this as a liquid instead of the standard powder?

    • Hi Ballanmessi,

      The dose of praziquantel would depend on the product you use, as it can vary in concentration between manufacturers. The dosage of 10g per 1000 gallons is just for Aqua Prazi treatments, and may be different for other brands.

      Sadly, I’m not sure where you can find praziquantel in Singapore. Your best bet would be to contact local aquarium/pond dealers and ask if they can help you further. Alternatively, you can contact Aqua Meds and ask them direct:

  1. Hi, my koi has fluke . I took her to the hospital and she was given a shot and the Aqua Prazi. But so far she hasn’t improved. She doesn’t move and looks to be opening and closing her mouth. Sometimes gasping and looks like she is spitting water out of her mouth . Any advice?

  2. Hi..I’m wondering if the temperature of the water is important to treatment with Praziquantel. If the water drops into the 40s, is it still ok/effective to use..? Thanks!

    • Hi Cherisse,

      Praziquantel will still be effective against adult flukes in cold water, so using it should not be a problem. When the surrounding water becomes very cold, the eggs of new parasites just take longer to hatch, so you may see a second outbreak in future when temperatures begin to rise. Dosing praziquantel at the start of Winter (or at first signs of flukes), and then again just before Spring, is good practice to keep them under control.

  3. When treating with prazi, do you keep feeding the fish the same amount you were feeding them before the treatment? Are you supposed to reduce the food the first few days?

    • Hi Mattie,

      Both food and medication will contribute to a ponds waste levels, which can have a negative impact on water quality if your filtration and water change routine isn’t up to standard. With that said, I’ve personally found prazi to have very minimal effects on water quality, so I think it should be fine to continue feeding as normal. You can check water quality after the treatment is complete, and perform a larger than normal water change if needed to reduce any excess nitrogen compounds that may have built up during the treatment period.

  4. Does Prazi affect test results? Five days after the second dose of Prazi my test kit shows strangely low results. Or does it affect ph and kh directly?

  5. I recently bought my goldfish chichi and I found out that she has a fluke. I never knew that praziquantel is a chemical-based treatment that has to be dosed correctly for it to be effective. It’s best if I’ll start looking for a shop that supplies this kind of treatment.

    • Hi Rachel,

      I’m glad that the article was helpful to you! Yes, any treatment, even if it’s not chemical-based, should be dosed properly to ensure that there is no damage to the fish, any other pond inhabitants, or overall water quality.

      Thanks for reading and commenting!

    • Hi Mike,

      Thanks for reading! It’s not recommended to use these two at the same time, as the combination of them can be too much of a hit to your fish and potentially result in other health issues. They may also damage water quality when used in tandem by killing off helpful bacteria in the water.

  6. Hi,

    It took me a few weeks to decide to treat with prazi. First I tried salt, did not work. Then I did a 3 day treat with microbe lift Broad spectrum disease treatment with water changes. Finally I added 40 grams of prazi mixed with the BSDT to help it mix in the water better as per directions I received elsewhere. My plan is to do a second prazi dose mixed with BSDT and then finally do a treatment of Dimilin 4 days after the second prazi treatment. I was thinking since the larger koi seem to be struggling more, should I also treat with a wide range anti bacterial? If so, when do I start that within my treatment plan and what anti bacterials do you reccomend other than melafix? My pond is 4000 gallons. Thank you so much for your time.

    • Hi Eric, i’m currently in the same boat that you were in. I did a Proform C treatment for 3 days with 25% water changes in between, and on the third day (today) i threw in Prazi with the Proform C as recommended on a Koi farm website (they called it a shotgut treatment).

      I’m curious as to how long after your Prazi treatment, you added Melafix? I’ve read that Prazi is only effective in the water for 48 hours so i was thinking of adding Melafix in 2 days to aid with the wounds left by the flukes on 3 of my big Koi.

      Hopefully you get this and have some insight

  7. How many days do you treat a 2500 gallon pond with the Eco-lab product. I was told to do a 25% water exchange daily for one week. After each treat add 8 ounce of the eco-lab microbe lift treatment. Does this sound accurate?

  8. This is one of thr best articles I’ve seen anywhere to help Koi owners like myself maintain a health pond and ecosystem but where can I get these products as no outlets where mentioned and I need to buy a few of these now.

  9. Hello
    I noticed in your very informative article in the information listed for Aqua Prazzi there is a typo?
    Notes 10gram per 100 gallons?
    Vs 1 gram per 100 gallon.

  10. Gill flukes keep coming back within a week of treatment. 3 treatments so far and just noticed they are back again!

    My water quality parameters all test fine. Well filtered pond.

    I added new fish a while back, may have been the source.

    Temp of water is a fairly constant at 60.2 degrees. Is the cold water just the right temp to allow eggs to keep hatching periodically?

    Using PraziPro.

    Appreciate your help and ideas!

  11. This is Tucker again. It is now January 11th. Been treating with Fluke M, too. Eggs keep hatching. Impractical to heat 75 degrees. Heating ti 60.5 degrees. Maybe I should buy stock in PraziPro or Fluke M. And yes, it is gill flukes since the reaction to treatment is effective. Any ideas would be appreciated!


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