Cotton Wool Disease in Freshwater Fish

Causes, Treatment, and Prevention

Guppy with fuzzy growth on dorsal fin

Flickr/Alice Chaos 

Cotton wool disease, also known as cotton mouth disease, columnaris disease, saddleback, and black patch necrosis, are all descriptive names for the same bacteria, columnaris (Flavobacterium columnare). This bacteria is commonly mistaken for a fungus, given its pale color and raised appearance. It can infect most species of freshwater fish but is usually secondary to another primary stressor. Some strains are more deadly and contagious than others.

What is Cotton Wool Disease?

Cotton wool disease is caused by the bacteria Flavobacterium columnare. It is not a fungus, despite its fungus-like appearance. It can infect the skin and gills and is of great importance to the commercial aquaculture market. It is rarer in the pet fish community. It is mostly an opportunistic pathogen that takes advantage of a stressed fish with a compromised immune system. There are many strains within the species, some of which are significantly more deadly and spread more easily.

Symptoms of Cotton Wool Disease in Freshwater Fish

The signs of cotton wool disease are usually noticeable since they are visible, but can often be confused for other fish maladies. The development of fluffy appearing skin patches will be the most obvious sign of the disease. Here is the complete list of symptoms:


  • Skin patches
  • Pale gills
  • Lethargy
  • Difficulty swimming
  • Loss of appetite

Skin Patches

The most common clinical sign of cotton wool disease is a pale, raised patch on your fish's skin. It can be anywhere on the body, including the face, mouth, and fins. These lesions typically have a fluffy appearance similar to a fungal growth.

Pale Gills

In some instances, these skin patches can spread to the gills. The gill tissue may then appear necrotic or pale when examined.


As the bacteria replicates and spreads throughout your fish's system, your pet will feel stressed and lethargic.

Difficulty Swimming

The spreading illness and patches can cause your fish to lose its equilibrium and cause it to have difficulty swimming.

Loss of Appetite

A sick fish often experiences a loss of appetite.

Causes of Cotton Wool Disease

Columnaris bacteria are commensal bacteria and occur naturally on healthy fish. The fish begin to show clinical signs if it is stressed out or if the strain of bacteria is particularly nasty. The bacteria commonly enters a healthy system when infected fish are added to the tank without the proper quarantine. It is critical to keep a close eye on your tank's temperature, since columnaris bacteria love warmer water (around 80 degrees Fahrenheit) which will cause problems faster than if they were present in cooler water.

Diagnosing Cotton Wool Disease in Freshwater Fish

It is critical to differentiate columnaris species from a fungal infection. To do so, your veterinarian will take a small biopsy from a sedated fish and place it under a microscope. If it is indeed cotton wool disease, the bacteria rods will form themselves into tiny haystacks, whereas fungus will not and the individual hyphae (branching filaments that are parts of a fungus) may be distinct.

Additional testing may be warranted by sending a swab sample to a lab to identify its strain and understand which antibiotics will be most effective. Never "guess" with antibiotic treatment. You may end up wiping out your biologic filtration and using the incorrect product or dose, breeding more resistant strains in your system.


All fish showing symptoms should be isolated into a hospital tank. Your veterinarian will prescribe an antibiotic to be added to the water or provide an injectable treatment. Injectable antibiotics will not affect your biological filter and they provide a stronger treatment option. Never attempt to inject your fish yourself.

Your fish may require different antibiotics if no sample is sent for culture and sensitivity testing. A detailed history of your fish including what treatments have already been attempted is critical to deciding which antibiotic is best for your situation.

Prognosis for Fish With Cotton Wool Disease

Severely sick fish, including those with greater than 50 percent of the gill tissue affected, may require euthanasia. It is very hard for fish to recover from such a severe infection. If your fish's gills have become infected, it is critical to give them additional oxygen support from an airstone.

Since it is a secondary invader, your fish system should be assessed for any potential stressors. This includes testing your water chemistry, reviewing your fish's diet, comparing fish compatibility, and examining any recent additions of fish or decor. If you do not remove the primary cause, your fish will get sick again after finishing treatment.

How to Prevent Cotton Wool Disease

As with most diseases, cotton wool disease can be prevented with proper quarantine. Take these steps to keep cotton wool disease out of your tank.

  • Quarantine: Set up a completely separate system with separate filtration and other equipment for four to six weeks. Two weeks is not adequate time and maintaining the correct temperature in a tank is very important.
  • Observe: Watch your fish closely during this time and note changes in their appearance and behavior. If you notice something wrong, it is critical to get it diagnosed fast and correctly to make sure it doesn't become a larger problem. By keeping your fish in isolation, you will protect your main system from infection.
  • Eliminate stress: It is also critical to keep your fish healthy in a low-stress environment. Make sure all fish have plenty of room to swim, a high-quality diet, and good water chemistry.