In the Edo period (1603-1867), the shogunate restricted fishing to the government's territory and imposed restrictions on the size of boats. Under these restrictions, basic fishing methods were established: seine nets were used on shallow sandy beaches where large nets could be easily drawn; line fishing was used on rocky or stony beaches unsuitable for seine nets; and fixed shore nets were used in fishing grounds where the topography and ocean currents resulted in large fish populations.

In Kujukuri-hama on the Boso Peninsula, sardine seine fishing started mainly among itinerant fishermen from Kishu (in present-day Wakayama and Mie prefectures). Since Kishu's mountainous terrain is close to the sea, there was originally little arable land. Furthermore, the farmlands were devasted by the long war, so the second and third sons of farmers found a way to make a living by fishing.

There are two types of seine nets: "double-handed", in which two boats work together to surround a school of fish, and "single-handed", in which one end of the towline is fixed to the shore and the net is laid by a single boat. At Kujukuri-hama, double-handed method was used, and about 200 people would haul the nets onto the beach, where most of the sardines were transported by boat to Osaka as hoshika (dried sardines) to serve as fish fertilizer for cotton farming.

Since ancient times, the Ainu people of Hokkaido have used nets to catch herring. Meanwhile, the Matsumae clan introduced "gill net fishing", in which nets are spread along routes taken by the fish, catching the fish by entangling them in the net. Gill net fishing was the method of choice during the spring spawning season. 

The farming of oysters began in Hiroshima Bay in the early years of the Edo period. Oysters were seen growing naturally on rocks along the shore of the Inland Sea, so someone came up with the idea of tossing rocks into the sea to get oysters to attach themselves to the rocks. Later, the "hibitate method" was developed (in which oysters were farmed by attaching oysters to bamboo or tree branches placed in coastal mud flats). By the mid-Edo period, oysters were being shipped to Osaka in "oyster boats" and it developed a monopoly on sales rights. Oyster boats went to Osaka in autumn, with oystermen mooring their boats at the foot of bridges on the Okawa and Dotonbori rivers to do business on board or in huts scattered along the riverbank.

Also, during the mid-Edo period, in an approach similar to oyster farming, a technique was developed in Omori in Edo Bay to create narrow gaps in shallow water in which seaweed with spores would grow. This cultivated seaweed was sold in front of the Kaminarimon in Asakusa (the "thunder gate," which remains a landmark in present-day Tokyo), and was known as "Asakusa nori."

As the season for each kind of fish approached, villagers would watch and wait in fishing huts for the fish to come in. Villagers who made a living by catching seasonal fish would prepare for the season by splitting their time between rice cultivation and dry-field crops. When a school of fish appears, the entire village went out to catch them. 

In years past, groups of fishermen in Northern Kyushu and in the Seto Inland Sea lived on board ebune, or scow houses. These fishermen fished in small fleets of boats, each consisting of several households, and made their livelihoods by bartering their catch for crops in the farming villages near their anchorages. Although they did not own land or houses, each group had its own headquarters and gathered for New Year's, the summertime bon holidays, and other festivals. 

After the Meiji era (1868-1912), these floating fisheries became more settled over time and lost their original form, but the culture of having a boat to sleep in and of couples who fish is still practiced in Nojima (Hiroshima Prefecture) and other places. 

Okikamuro Island in Yamaguchi Prefecture is a small island in the Seto Inland Sea having a circumference of 5 km. It is connected to Suo Oshima by the Okikamuro Bridge (opened in 1983), and had a population of 96 as of 2020 (national census). The island is surrounded by mountains, and the residential area is packed densely into a small flat area by the sea. 

The surrounding area has had excellent fishing ground since ancient times, and fishermen thrived on sea bream single hook fishing using the nationally renowned "kamuro hook." Many fishermen moved to the Okikamuro Island, and by the Meiji era, the population exceeded 3,000, and in those days the island was known as Kamuro Senken.

Okikamuro Island is known as the "island that sinks during the Bon holiday." This means that many people from this small island and their families return home during the summertime Bon holiday to make the island sink. The name was originally given during the Meiji era when men who went fishing in distant places and did not live on the island except for the Bon festival returned to the island en masse. 

Fish finders, which convert ultrasonic signals bounced off fish into images, were invented in Japan soon after World War II in 1948 and have been in use ever since. At the time, it was only used to identify fish species and size of the fish population. However, in recent years, detection technology has advanced to the point where it is now possible to determine the number and size of fish (quantitative echo sounder).

There are various gods of fishing, such as the Dragon God, the Water God, and Funadama, who are the object of prayers for bountiful catches of fish, and Ebisu, one of the Shichifukujin (Seven Gods of Fortune) is one of them.