There are differences in the length distribution of carp excavated from Jomon and Yayoi sites, as estimated from the size of their pharyngeal teeth. Specifically, not only adult carp but also juvenile carp (less than 150 mm in length) have been found at the Yayoi site. This difference is thought to be due to the fact that the Jomon only collected carp from lakes and rivers, while the Yayoi cultivated primitive carp along with the spread of rice paddies.<ref name = "Nakajima2011" /><ref name = "Nakajima2010">{{Cite journal |last1 = Nakajima |first1 = T. |last2 = Nakajima |first2 = M. |last3 = Yamazaki |first3 = T. |title = Evidence for fish cultivation during the Yayoi Period in western Japan |journal = International Journal of Osteoarchaeology |volume = 20 |issue = 2 |date = 2010 |pages = 127–134 |doi = 10.1002/oa.1005 }}</ref>
It was previously thought that all Japanese carp were introduced from China in prehistoric times.<ref>{{Cite journal |last1 = Jordan |first1 = David Starr |last2 = Fowler |first2 = Henry W |title = A review of the cyprinoid fishes of Japan. |journal = Proc. U.S. NatNatl. Mus. |issue = 1334 |date = 1903 |volume = 26 |pages = 811–862 |doi = 10.5479/si.00963801.26-1334.811 |url = https://www.biodiversitylibrary.org/part/9451 |access-date = 4 January 2024 |archive-date = 14 March 2023 |archive-url = https://web.archive.org/web/20230314064516/https://www.biodiversitylibrary.org/part/9451 |url-status = live }}</ref> However, recent analysis of [[mitochondrial DNA]] has revealed that there are two types of wild carp in Japan: native carp and [[Cyprinus rubrofuscus|Amur carp]] from Eurasia, but it is unclear when the Amur carp was introduced to Japan.<ref name="onlinelibrary.wiley.com">{{Cite journal|last1=Mabuchi|first1=K.|last2=Senou|first2=H.|last3=Suzuki|first3=T.|last4=Nishida|first4=M.|date=June 2005|title=Discovery of an ancient lineage of Cyprinus carpio from Lake Biwa, central Japan, based on mtDNA sequence data, with reference to possible multiple origins of koi|url=https://onlinelibrary.wiley.com/doi/10.1111/j.0022-1112.2005.00676.x|journal=Journal of Fish Biology|volume=66|issue=6|pages=1516–1528|language=en|doi=10.1111/j.0022-1112.2005.00676.x|bibcode=2005JFBio..66.1516M|issn=0022-1112|url-access=subscription|access-date=3 October 2023|archive-date=10 October 2023|archive-url=https://web.archive.org/web/20231010105228/https://onlinelibrary.wiley.com/doi/10.1111/j.0022-1112.2005.00676.x|url-status=live}}</ref> This is because the oldest record of the introduction of non-native fish in Japan is that of goldfish from China (1502 or 1602),<ref>{{Cite book |editor = Kokusho Kanko-kai |title = 雑芸叢書 |trans-title = Miscellaneous Art Series |volume = 1 |publisher = Kokusho Kan-kai |date = 1915 |doi = 10.11501/1869566 |page = 265 |author1 = 国書刊行会 }}</ref> and there is no record of carp (including colored carp) until the introduction of the [[mirror carp]], called ''Doitsugoi'' (German carp), in 1904.<ref>{{Cite book |last = Maruyama |first = Tamezo |title = 外国産新魚種の導入経過 |trans-title = Progress of introduction of new foreign fish species |publisher = Fisheries Agency, Research Department, Resources Division |date = March 1987 }}</ref>