As you begin to shop for koi, you'll notice a great difference between the price of domestic koi and Japanese koi. You'll also notice the difference in color, quality and beauty. Japan is the birth place of the modern koi, and they have been raising them for 200+ years. Japanese koi breeders are experts in what makes a prize fish, and that joined with cost of shipping and handling creates the price difference. Some Japanese koi can sell for hundreds, even thousands of dollars, so a good Japanese koi can be a great investment. Put a Japanese koi and a domestic one side by side and you can usually see the difference in lustre even to the point where the Japanese fish appears more vivid, like putting a royalty next to a common peasant.
That isn't to say that Domestic koi aren't worth owning. On the contrary. It is possible to raise a domestic koi that is every bit as indistiguishable from it's Japanese counterpart, and even if it won't win any koi shows, you can still fall in love with it just as easily as a fish you pay hundreds for. And, like buying a new car compared to buying a used one, you don't have worry as much about the outcome if you do something wrong. If you haven't had a pond for long, you may not want to invest hundreds of dollars on fish you aren't sure you can keep alive! And remember, the babies born from Japanese stock are still domestic, but with good water quality, they sure can be pretty!
