It is said that since the Jomon Period (14000-300 BC), people have piloted dugout canoes from the islands of the Japanese archipelago out to sea to catch fish. Fishing equipment in those days included fishhooks and harpoons made of wild boar bones and deer antlers, and nets woven from plants.  Across Japan, archaeologists have excavated many stone weights that were used for sinking nets.

The Jomon people also collected littleneck clams and hard clams on tidal flats, and white clams in brackish water near river mouths (where fresh water and seawater mix). By fish bones excavated along with shells from shell middens indicate that the Jomon people also ate horse mackerel, sardines, mackerel, red sea bream, black sea bream, sea bass, bonito, tuna, and Spanish mackerel from the sea, along with such river fishes as carp, crucian carp, and eels.

A number of small jar-shaped earthenware vessels penetrated with holes have been excavated from Yayoi archaeological sites along the Osaka Bay and Seto Inland Sea coasts. These jar-shaped vessels were used as octopus traps, similar to the octopus trap pot fishing which is practiced to this day. In octopus trap pot fishing, a string is threaded through holes in the jars, several of which are connected and lowered to the seafloor. Octopuses like to conceal themselves in tight spaces, so the jars are usually full of octopuses when they are hauled back up to the surface. Based on its size, the earthenware excavated at the Yayoi archaeological site is assumed to be a jar for catching ocellated octopuses (a small octopus about 20cm in length).

The ancient practice of fishing in rivers and lakes is recorded in the Kojiki (8th century "Record of Ancient Matters") and the Manyoshu (the 8th century collection of classical Japanese poetry).

This poem means that there are many obstacles to love, just as the flow of the rapids in a river where the Ada people set fish traps, so I think of you in my heart, but I can't meet you directly.

Weirs are screens made of wood or bamboo, and fish weirs are set up across the river to catch the fish that landed on the screens. Ada is current Ada area in Gojo City, Nara Prefecture. The rapids in which the fish weirs were placed are in the Yoshino River, which is famous for ayu (sweetfish). 

In the Kojiki, the god Kunitsukami (son of Niemotsu) is described as catching fish in the Yoshino River with a cylindrical fishing basket (made of bamboo or twigs bound with vines and closed at one end). 

Various fishing methods were created and developed in rivers and lakes from ancient times to the Middle Ages. These traditional methods of fishing with weirs and bamboo fish baskets are still used today in many parts of Japan. 

During the Heian period, the population increased and occupations became more differentiated. As a result, fishing emerged as a livelihood, where fishery products were exchanged or redeemed for other daily commodities, and seafood became specialty products.

Among the taxes levied on localities under the Ritsuryo system, chou were either textiles used as a substitute for money or local specialties. The Engishiki (detailed regulations for the implementation of the Ritsuryo system) records that a wide range of marine products and their processed products, such as bonito from the Pacific coast as well as abalone and kombu (kelp) from various regions of Japan, were delivered to the capital as tribute. The aristocrats of the Heian period used the best seafood from all over the country as ingredients for their sumptuous meals, which included a wide range of grilled fish and steamed abalone as main dishes, along with seaweed soup.

Approximately 1.5km long on its southeastern axis, Okishima Island (Omihachiman City, Shiga Prefecture) in Lake Biwa, Japan's largest lake, is the country's only inhabited island in a freshwater lake. The ancestors of today's islanders are believed to have been warriors of the Minamoto clan who fled to the island after being defeated in the Hogen and Heiji Wars during the Heian period (794-1185). 

In the Azuchi-Momoyama period (1568-1600), feudal lord ODA Nobunaga granted exclusive fishing ground privileges to islanders who had distinguished themselves in battle. These privileges endured for an astonishing 400 years. Even though the islanders lost this privilege with the revisions of the Fisheries Law after World War II, the island still boasts approximately 40% of the total catch of the Lake Biwa fisheries. 

In these ancient times, seine nets were commonly used, and nigorobuna and moroko (both members of the carp family and native to Lake Biwa), as well as funazushi, a fermented crucian carp sushi made from nigorobuna, developed as specialties of the region. Another characteristic of Okishima is the variety of fishing methods used according to the seasons and species of fish, including the traditional "weir fishing", a fishing method in which nets are cast from the lakeshore in the water to steer ayu and crucian carp into a ceramic jar.