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I own 2 Raphael catfish and 4 koi, everyone has been happy for the past 2 months but recently i noticed one of my rapael's top half of his mouth is completly missing!! and my largest koi has a red/swollen upper lip, ill try to upload pics, (im new to this forum thing) i really need to know what to do, i can't bring myself to flush my raphael while he is still alive, and i cant stand to see him sulk around the tank all day, IMG_20140108_195830.jpg
 

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Hi linkqwertyui and welcome to the forum. I'm sorry about your raphael catfish. They're such handsome critters.

First, I need to ask some questions. How long have you kept the koi and the raph together? What size is the tank? How often do you perform water changes?

The reason I ask is because first, koi are coldwater fish. They do not do well in temperatures over 72 or so, especially for extended periods of time. Right now, my three koi are outside in a pond with a temp about 50 or so for the winter. The problem with keeping the koi and the raph together is raphael catfish are definitely tropical fish and require temps around 78. You can see the conflict here. :(

Secondly, koi get very large and produce prodigious amounts of toxic ammonia. I would not recommend keeping multiple koi in anything less than three hundred gallons with a very strong and effective filter. They produce a great deal of waste and their homes require an effective biological filter.

That all said, I suspect that both of your fish are suffering from ammonia/nitrite/nitrate poisoning and burns with secondary bacterial infections. When ammonia levels go above .25ppm, the fish begins to experience discomfort. As the levels climb higher, that discomfort manifests itself as burns which can become infected and begin to eat away at the flesh. The same thing happens with high nitrite and nitrate levels. It would be a good idea if you tested for these levels.

I suggest you remove the raphael to his own tank for treatment; while you are treating him, you may want to consider rehoming the koi or relocating them to a deep pond outside.

To treat both the raphael and koi, I'd suggest using API Pimafix and API Melafix combined. Use an airstone to create extra oxygenation during treatment.

I hope this helps. Please keep us updated.
 

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hopefully with treatment the rafael will be ok.
 
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