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CPD are pretty common. Most FW fish are farmed so not many are considered rare. Bred out mutations and variations of species though are a different story like in the case of Koi and Arowana.
 

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I believe true zebra plecos prefer sand or fine gravel and a good amount of caves more than plants, but I could be wrong. What about botia sidthimunki (or Yasuhikotakia sidthimunki, dwarf loach by its other names)? I can find them locally on special order, but most places have never heard or seen them, but that would probably be different elsewhere.
 

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Green Flash, are you specifically just looking for a very small rare fish? Or are we talking about rare fish in general regardless of size.

I guess it depends on the area you live in. Where I am I would consider Rasbora Briggitae pretty rare. I never see them in stores and would love to get some eventually.

There also seems to be a lot of beautiful variation in the killifish family, and I NEVER see them in stores.

Another rarity that comes to mind is the surface dwelling form of the blind cave tetra (the non-blind form with silver scales and red fin pigment). I would love to get my hands on some of those, even though they aren't considered particularly remarkable.
 
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