The carp is a large group of fish originally found in Central Europe and Asia. Various carp species were originally domesticated in East Asia, where they were used as food fish. The ability of carp to survive and adapt to many climates and water conditions allowed the domesticated species to be propagated to many new locations including Japan. Natural color mutations of these carp would have occurred across all populations. Carp were first bred for colour mutations in China more than a thousand years ago, where selective breeding of the Prussian carp (Carassius gibelio) led to the development of the goldfish.

Carp are known as koi in Japan. Of the various domesticated carp species, the common carp (Cyprinus carpio) is one of the more commonly used in aquaculture. Common carp were first introduced into Japan by way of China between 400 to 600 years ago. Common carp were first bred for colour in Japan in the 1820s, initially in the town of Ojiya in the Niigata prefecture on the north eastern coast of Honshu island. By the 20th century, a number of colour patterns had been established, most notably the red-and-white Kohaku. The outside world was not aware of the development of colour variations in koi until 1914, when the Niigata koi were exhibited in the annual exposition in Tokyo. At that point, interest in koi exploded throughout Japan. The hobby of keeping koi eventually spread worldwide. Koi are now commonly sold in most pet stores, with higher-quality fish available from specialist dealers.

Extensive hybridisation between different populations has muddled the historical zoogeography of the common carp. However, scientific consensus is that there are at least two subspecies of the common carp, one from Western Eurasia (Cyprinus carpio carpio) and another from East Asia (Cyprinus carpio haematopterus). One recent study on the mitochondrial DNA of various common carp indicate that koi are of the East Asian subspecies. However another recent study on the mitochondrial DNA of koi have found that koi are descended from multiple lineages of common carp from both Western Eurasian and East Asian varieties. This could be the result of koi being bred from a mix of East Asian and Western Eurasian carp varieties, or koi being bred exclusively from East Asian varieties and being subsequently hybridised with Western Eurasian varieties (the butterfly koi is one known product of such a cross). Which is true has not been resolved.