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  Japan has so many fish in both freshwater and saltwater. Among fly anglers, trout family is the most important, common and popular but nowadays people never stop trying to catch new species. We have some native trout, char and salmon but introduced trout such as rainbow trout, brown trout spread out and become wild in many places.

Areas close to big cities where a lot of people come have way less native/wild fish but many of those rivers are stocked with hatchery fish every year. Basically you pay 500-2000 yen for a one day fishing license or 3000-10000 yen for a yearly license, depending on the local fishery regs. In most cases the fish raised in the hatcheries have injured fins and scars all over the bodies so anglers prefer the wilder fish to those injured fish. For this goal, avid anglers near Tokyo drive a long distance to areas like Tohoku (northern mainland), Hokuriku (Japan sea side) and other rural areas.
Typical concrete rivers. Still many fish but oh well.
  Somehow government wants to put man-made structures in many rivers. There are a whole bunch of bullshit about flood control and stuff but a lot of money is involved. Seeing those artificial rivers makes us nothing but sad.  
  The ultimate destination for trout fishermen would be Hokkaido. Hokkaido rivers are basically open year-round without a fishing license needed. There are plenty of wild native species and transplanted species. Sapporo, the capital of Hokkaido with a 1.8 million population, is a big city but if you drive a couple of hours, you can have many fishing spots all to yourself on weekdays. Northern and eastern Hokkaido have way less people and the fishing environment is literally rich in many ways. Size of the fish, number of the fish, condition of the fish...all desirable. Many people living in the mainland and other areas fly to Hokkaido from spring to autumn with some die-hard anglers flying in winter time. Targets vary from rainbow trout to salmon.  
Common trout stream scenery
  In Japan probably the most sought-after fish by fly anglers would be yamame, landlocked cherry salmon. Although they are called salmon, we regard them as trout. This petite fish attract not only fly fishermen but also lure fishermen and bait fishermen. However the number of the fishing spots where you can catch wild yamame is on the decrease, so we have no choice but to aim at hatchery fish. Thanks to the development of the aquaculture, conditions of the hatchery fish look good but still some purists don't hesitate to climb mountains to reach dangerous spots where pure native fish live. However yamame don't live in the headwaters so it is difficult to find pure native yamame nowadays.

Yamame is land-locked so they don't migrate. Or maybe anglers catch and bother them so they cannot migrate freely. Also Japan has so many dams and weirs, which block fish migrations. Yamame live in freshwater lakes, which we call sakura-masu. Sakura-masu is originally cherry salmon which migrate form the ocean and spawn but however we call lake-dwelling yamame sakura-masu as well. River resident yamame have parr marks even after they get mature but generally speaking lake dwelling yamame, sakura-masu look shiny with no parr marks. They are strong and can be up to 60cm so anglers chase those precious gems.

A close kin, hon-masu lives in Lake Chuzenji. Their body is chrome silver and very beautiful. Amago is another close kin living in western Japan. They have orange dots over the body so you can identify them but they look very close to yamame.

Cherry salmon , ocean-going sakura-masu, is rare in Honshu due to overharvesting, civilization, etc. They go down to the ocean to grow big and come back around cherry blossom season. Its difficulty makes many anglers crazy about the fish but a few fly anglers catch them every year. In Hokkaido there are a lot of sakura-masu even today but it is illegal to catch them in freshwater. You can catch and eat them in saltwater but you cannot in rivers. In most cases sakura-masu in Hokkaido lakes are ok to target.
  Iwana, a kind of char native to Japan, is another popular fish living in the headwaters. There are still many native iwana across the country because they live in mountainous ravine areas, which can make it hard for humans to reach. There are legends about huge iwana seen by local old timers in each watershed. Iwana live in rocky ravine areas so it tends to be associated with trekking and adventure. They are aggressive so many dry fly fishers love this fish. In summer quite a few people go to the headwaters to meet those ninja fish in steep valleys.  
Typical rocky headwaters which hold a lot of iwana char.
  Rainbow trout were introduced to Japan as food over 100 years ago. It is often said that this fish cannot spawn properly in Japanese streams for some reason, but apparently we see wild rainbow trout in some areas. Especially in Hokkaido, there are many wild rainbows, like successfully introduced rainbow trout in NZ. In Hokkaido many people regard rainbow trout as the best target due to its strength and fight. On the contrary near Tokyo rainbow trout can be undervalued, because most rainbow trout are hatchery fish with many injured fins. Rainbow in Hokkaido is almost the same as native one in North America but rainbow near big cities are like sardine in a fish pen. You know what I mean? Fins have scars and they are not strong. So some people don't appreciate rainbow trout but appreciate yamame and iwana. Interesting but Hokkaido people don't really understand this. Fisheries in lakes used to stock the lakes with morbid rainbow trout. I guess quantity was important more than quality. But for the past decade, people's demand changed and fisheries started to understand. They let beautiful hatchery fish in.

Wild rainbow trout can be 70-80cm in Hokkaido, which is a real gem. But it is not easy to catch those monsters. If you catch a 50cm fish, you should be very happy. If you catch a 60cm fish every year, you should thank your God. If you catch a 70cm one, your luck might have been over. Hardly any people have caught a 70cm rainbow. A rainbow over 10lb would be a big fish for any North Americans I reckon, though.
Typical urban fishing ponds. Even some swimming pools become fishing ponds from early winter to next spring.
  In Japan there are quite a few private fishing ponds and streams stocked with hatchery fish. Especially around big cities, those fishing ponds are popular to satisfy fishermen who are eager to catch bigger fish. The most common fish in those fisheries would be rainbow trout. In those ponds, you are almost promised to catch some fish. The fishing fee is 3000-7000 a day in most places. The quality and conditions of the fish and the water are not bad at all nowadays. Some private fishing ponds are set in natural lakes so you can enjoy the scenic fishing through the day. However urban ponds are not beautiful. Just a place to catch fish. You can kill and bring fish home in many places.

  Brown trout is also popular but wild browns are not so common across the nation. In Hokkaido and some parts of mainland have a healthy population of brown trout. Reports say wild Hokkaido brown trout grow up to 100cm. As they eat baitfish voraciously, this fish tends to be controversial and some cities try to annihilate them. For the moment it is illegal to carry live brown trout in Hokkaido. You can fish, catch and release, or kill and take it home to eat but cannot move live brown trout to another water. The police an bust you so you must not try it. In 2013 Hokkaido government announced that they are thinking of putting rainbow trout in the harmful foreign animal list, too. If they make a new law, we cannot carry live rainbow trout without permit. It is quite controversial for anglers. Unless we can restock rivers and lakes with rainbows, we might lose rainbow in the far future in Hokkaido. We will see.  
  If you chase trout, you are likely to see some coarse fish. The most common one is called ugui. It is in a carp family. They don't fight strong so people don't appreciate. In Honshu there are some other fish but oikawa is a beautiful fish with long fins. They live more downstream than trout live so you won't see many of them while fishing for trout but some people target oikawa, as they are closer to urban areas and easy to get there.  
Chum salmon and pink salmon came back.
  Salmon is popular as the seasonal meat among all types of fishermen. In Hokkaido fly fishers may have a hard time in casting because very many people gather in popular spots so there is no/few spaces enough to cast near big cities. The eastern Hokkaido is less populated so you should drive to east. Gear fishing may be better to catch salmon effectively in a crowd.

It is illegal to fish for salmon in freshwater except in some rivers. The police will get you so never fish for them in rivers, even though you will see thousands of them swimming. There are a handful of rivers where you can fish for them on a license basis. You need to apply for the license and have to win it beforehand. It costs you around 5000 yen a day. This system started in the 90's then it was dramatic change so people rush to the lottery. Nowadays it is not super popular so you can reasonably win the license. There are a few in Hokkaido and some in Honshu Island.

We only have 2 salmon but maybe cherry salmon should be counted so we have 3? 2 are chum salmon and pink salmon. We don't have coho, chinook or sockeye.

You can fish those salmon in saltwater with no cost.
  Large mouth bass have been extremely popular among lure fishermen for about 40 years in Japan with the peak in the 90'. Their aggressive manner captivated fishermen but new problems surfaced up in the 90's and 2000's. Bass and bluegill pan fish eat Japanese native fish, which was a huge problem for commercial fishermen and from the environmental point of view, people started to regard them as enemies and a great threat to Japan. Some prefectures set new laws which prohibit us from releasing fish back to the water. It means you have to kill bass after you catch them. This is very controversial. Small mouth bass came to Japan way later than large mouth bass and acquired similar popularity. They live in cooler waters so the habitats are limited in numbers. This cold water species is a big threat in the trout lakes and rivers.

You can find large mouth bass and bluegill almost anywhere in Honshu and west. They are warm water fish so cannot live in Hokkaido but it seems that some spottings were reported, although I have personally never seen them in Hokkaido.

If you live near Tokyo, it is easy to go to bass fishery, as there are a lot. Generally speaking bass fishing is free. Access is all you overcome. If you reach the bass lake or river, you can do whatever you like. If you live near in Osaka, lake Biwa, the biggest freshwater lake in Japan, is quite famous for bass fishing. You should go.

Most bass lakes don't need a fishing license.

  Let's talk about watercraft. Needless to say, it is much more effective to cover waters with a watercraft. Japan's roads are so narrow that it is difficult to tow a boat trailer. So a float tube or inflatable boat are easy to use. Some people use those boats for bass fishing. In Honshu many trout lakes ban private boats but in Hokkaido you can use your boat in most lakes and rivers.

Make sure to wear a PFD and fish with your buddies. Safety comes first.
  Carp is popular among urban fly anglers because their habitats are the lower muddy waters close to big cites. They grow big and can be selective to flies, some people are keen on carp fishing. They take dry flies and nymphs but bread flies are unique in this fishing. People (non-fishermen) feed them bread so fish are conditioned to bread in many urban areas.

They might look dumb but can be very canny and ignore flies. Can be leader-shy on a bright day in popular spots so your approach is very important. They make a school. If a fish's back touches a leader,
the fish can be spooked and panicked, which can send an alarm to the whole school. In that case, you lose the chance for a while. Once they become cautious, it is difficult to let them bite. Pretty smart fish.

Can be big up to 80cm so don't underestimate the power. Their fight is like that of chum salmon. They don't run fast but dogged fight lasts long. In most places you don't need a fishing license.
  Saltwater is a new field for fly anglers. Above all, suzuki,seabass, is a popular fish among lure fishermen and fly fishermen. They are big in size and act aggressively so many people living close to the ocean chase suzuki keenly. Lately there are some fishing boat charter services specialized in suzuki fishing around Tokyo and other urban areas. Seabass chase sardines and other baitfish so streamer fishing is common throughout the year, but sandworms are the seasonal delicacy in the spring. They come in a big group to the surface to lay eggs. Seabass eat them in frenzy. Under such situation, it can be easy to catch them on worm-like flies.

Rockfish is relatively easy target for beginners. They come close to the surface at night. You can use weighted flies on a floating line or a sinking line. Not really big but some of them fight aggressively. Tasty fish so catching them has another bonus. Be careful at night.

Beach fishing for hirame, flounder, is done by a few people. Suzuki can be caught on beaches but when you fish on beach, take an extra care against rays. They have a long sting with strong venom. It is said that they will sting you, if you step on it. In order to keep away from the trouble, keep your feet on the sand and drag them along the sea bottom so that you won't step on it. They say that rays will be gone, if you kick from side. But if you step on it, it can be the end of the world. They don't kill people often but if you have an allergy, you can be dead.

Off-shore boat fishing is popular among some fly anglers. Dolphin fish fishing is in full swing in mid summer. Its big size and aggressiveness captivate a lot of saltwater fans. This fishing often comes with motion sickness so you have to be good at a boat swaying up and down on a rough day.

Yellow-fin, billfish and other big game fishing can be done in western Japan but for the moment, we cannot say they are very popular. Only enjoyed by some fanatic anglers with some extra money. Not really common for average fly anglers.
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