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Cotton wool or cotton ball disease is a charming name for Saprolegnia — a nasty fungus that grows when bad water quality stresses your koi. Expect to find it when the water contains quantities of uneaten food and when the pond has too many koi for its size.
Fungus can attack any weakened portion of a koi, from the skin to the gills. It usually takes hold opportunistically, when the koi are stressed. Be sure that you always check for the presence of fungus when your fish suffer an unrelated trauma or illness.
When a koi has cotton wool fungus, the fish develops what looks like a fine-textured fur coat over its body that's actually mold growing on the skin. Sometimes the fungus looks like a pale-orange or ivory-colored layer. As the disease progresses, the fungus grows longer, cotton-like tufts.
Treat this disease by correcting the conditions that lead to the outbreak:
- Decrease the number of koi in the pond.
- Improve water quality via partial water changes; an upgraded filtration system; an ammonia remover like AmQuel Plus or Zeolite; and increased aeration.
 | You can also use medication against the fungus. Adding methylene blue (a dye commonly used as a fish medication and available at most pet stores) to the pond at a rate of 1 teaspoon per 700 gallons helps kill the fungus, but individually treating each affected koi in a quarantine tub stops the progression of the disease much faster. |
Either sedate the koi or hold it so you can remove the patches of fungus with a cotton swab. Then dab the affected spots first with malachite green (a fungicide) and then with propolis (an antibiotic and topical treatment). Return the fish to the quarantine tub and watch closely to make certain no secondary fungal or bacterial infection sets in.
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