For some species it is very important to keep it pure, namely fish that readily hybridise like Endlers crossing with guppies and many cichlid species interbreeding.
Many of the guppies that are breeding true to a particular colour strain or fin trait have literally taken years to establilsh (this is true for any species be it cattle/cats/dogs/shrimp), there will be many issues involved in trying to establish a breeding true species be it the odd throw back to another colour/ fin type and these undesired traits have to be culled from the breeding programs. Also with guppies there is the added problem of holding/ storing sperm by the females from previous matings. So any particular batch of babies could be from multiple males that the female had previously bred with. That is why breeders of particular strains will generally only breed a known quantity virgin female with a known quantity male, after her first breeding and subsequent fry drop that female may then be culled or only ever be kept with that one male for the rest of her breeding life.
As you can imagine the sheer scale of number of tanks needed, food quality, water quality, and time taken to sort sexes and pick the desired traits that goes into such a breeding exercise can run into the thousands of dollars mark.
The other reason to keep a species as pure as you can is if you breed say a guppy with an Endler there will be nothing wrong with the offspring but it is only fair and ethically correct to warn all potential future owners that the offspring are a mix not pure of either species. Unethical people may if say Endlers are the harder to get species pass off these mixed genetic fish as "pure" and the unwitting buyer then continues the falsehood of having "pure" endlers by accident. Shops may not even always pass on the genetic status of the fish they have purchased from members of the public, this is not always a deliberate ploy by the shops but an oversight because the one staff member who did know it was a hybrid didn't make the sale or was absent on the day of that particular sale.
Also by keeping a species (for this I am talking about rarer species than guppies) it is possible to re-introduce critically endangered species back into their natural habitat by using stocks that had been kept and bred pure in captivity. Even zoos are staring to have trouble ensuring that their breeding programs are keeping species true to form. I have heard of different orang-utan species being bred by accident in zoos, and it is even suspected that many of the tigers kept in zoos around the world are actually results of hybrids for example breeding a Bengal tiger with a Sumatran tiger. This was not necessarily done deliberately but by accident from when zoos used to send out their own trappers for zoo stock and people saw a stripey large cat which was close enough in markings and size to another stripey large cat from a similar country and just calling both big cats tigers.
