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World's busiest train station with 3.64 million commuters on average weekday. No spawn point on the huge station (36 platforms, 200 exits!) itself. Probably removed on demand. But there's a lot of spawn points outside of the station. The area is mostly commerces, restaurants, offices, entertainment. It's a good place for urban pokemon like [[Porygon]]. You'll mostly be catching things while walking in these busy streets, so try to not bump into other people.
===[[Yoyogi in Tokyo, Japan|Yoyogi]]===
A very large nest in west Tokyo, between Shinjuku and Shibuya. Directly out of the Harajuku station. You can usually catch 35 nest pokemon/hour (and not be able to go after every single one). Somehow, I always have a [[Snorlax]] spawning when I happen to go there. Often get a [[Farfetch'd]] too. Helped me a ton for [[Charmander]] and [[Growlithe]] [[candies]] since [[fire]] pokemons are a bit rare around here. A pond in the center will spawn a few [[Dratini]] during a farming session. A good number of pokestops too.
You can follow a looping footpath through the park. You can also cut anywhere in the park, but there isn't much footpaths to help to do so. Night falls early in Japan, so in December taking shortcuts (not lit areas) meant tripping every 4 meters on some tree root while farming Charmanders. By the way, the loud message repeating that skateboard/rollers are forbidden in the park and dangerous gets a bit annoying. You can't do it either in the street in Japan, but the cops will only tell you to not do it and you'll be fine if you stop. You usually only get warnings for minor offenses. In my home country, cops would usually fine you ~$50-$90 no matter what.
===[[Shibuya in Tokyo, Japan|Shibuya]]===
World's busiest crossing is there, with an estimated 2500 people crossing the street every time the green light switches on. It's also world's 4th busiest train station with 2.4 million passengers going through on weekdays. It's also well known because of the story of [[Hachjiko]], the dog who waited 9 years in front of the station for his dead master to return. Mostly shops and fashionable things.
People often stand in front of the building or near the shop's entrance. The store employees never tell people to leave, although the swarm of players is obstructing the way. If the weather is too hot or too cold, you might rather enjoy the AC at Mc Donald. It's not unusual for players to just buy the cheapest things on the menu (usually a coffee) and then sit for hours inside. Even in busy hours, you never get kicked out of Mc Donald. Mc Donald is also quite popular with high school student, who buy french fries + drink and stay studying in group for hours, or passing business men who work on their laptops. Well, in the case of PoGo players you can argue that McDo wanted you in their shop with their sponsorship, so they got you sitting there. McDo Japan had actually been on falling profits in recent years because of a few food scandals, but their results have gotten better since last summer.
===[[Meguro River in Tokyo, Japan|Meguro River]]===
It's a good location to farm [[Dratini]] around Tokyo. The alleys along the river are very quiet in spit of being in the city, and there is some nice cherry blossoms in spring. Pokemon clusters spawn all the way and there is always pokestops to spin. There is also a few small parks with nests on the side. Often encounter 5-6 Dratini per hour while grinding there. Even managed to encounter 6 Dratini in 5 minutes on a 25 meters section, one RNG lucky day. Actually, the abovementioned Shinjuku-Yoyogi-Shibuya and Meguro river are adjacent from north to south. So, someone up for a 3 hours walk can have a nice grind session through heavy street biome -> heavy grass biome + current massive nest -> mountain biome -> heavy water biome.
===[[Ueno Park in Tokyo, Japan|Ueno Park]]===
A very large park in Tokyo. It was founded during the Meiji era (19th century), when Japan was opening to the western world. The northern part of the park has many trees and footpaths and is a large pokemon nest.
In late September, it became forbidden to play in the temple area. Some players were still ignoring the messages though, or were just going through to trigger at lest the encounters. The pokestops have been removed since then. There is still Dratini, but it's not as interesting as it was back in summer, and this part of the park is now part of the nest rotations (the northern part was the only affected in summer), which means Dratini spawn points get ""cannibalized"" by nest species. I only farmed 3 times there in summer, but in the end the Meguro river gave me as much if not more Dratini per hour and was my daily grind anyway.
===[[Kinshicho in Tokyo, Japan|Kinshicho]]===
Wasn't anything out of the norm until around November, but the new sponsorships added even more stops than before and it's now a 9-permalure spot (the multiple floors station and its shops helped). But it mainly draw from street/grass biome, so you might prefer the 7 lures at Shibuya for mountain biome.
===[[Hibiya Parkin Tokyo, Japan|Hibiya]]===
A good-sized nest, with a small pond that will spawn a few Dratini. Expect to catch around 20 nest species/hour. There is a lot of footpaths in every directions, making it easy to go around. Pokestops all over, you always have one to spin while walking. There's also a 4-5 close pokestops spot that is often lured. The Tokyo Christmas market is held there, so in December you had the bright Christmas market in the center, and PoGo players lurking in the dark around it to farm [[Jynx]], who was the only practical way to get the ice medal in [[Gen 1]]. [[Ice]] types are still very rare in Tokyo in gen2, we don't really see wild [[Sneasel]] or [[Swinhub]] outside of nests.
===[[Trainer Spots in Imperial Palace East Garden]]===
A nest with a good spawn rate. Can get around 30 nest species/hour. Free entrance, but there is opening and closing hours. In this season, the place closes at 4:30pm and the last admission is at 3:45pm, so it's difficult to use if you work in weekdays. You're basically walking in a loop, with no shortcut possibilities. It's not that wide, so you're not going to miss any spawn.
===[[Odaiba in Tokyo, Japan|Odaiba]]===
An artificial island in the Tokyo Bay. Has a lot of shops, restaurants, entertainment utilities and exhibitions. There's also the Toyota City Showcase, where you can try cars, simulators and get a display of Toyota's technologies. People who are into manga probably know the Comicket, which is held at Odaiba's Big Sight. It's also home to the real size Gundam statue. It has been removed 2 weeks ago though, and will be replaced by an another Gundam model. Mostly a place for tourists though, Tokyo people are more likely to gather in other places during their spare time since Odaiba is a bit off the way.
Odaiba is quite large, so the best way to go around is to use the rental bike service. It's quite cheap and you can return the bike at a lot of stations. It's electric bikes, a breeze to use. The place can also be rage inducing because some spawns appear right into the sea, impossible to reach. I once tried to get my first Larvitar there. One eventually spawned in the sea, near an elevated ridge. Many players (including myself) disregarded the security barrier and went as close to the border as possible, in spite of a slippery slope. No luck. But 10cm more and it was a straight 10 meters fall into the sea.
===[[Akihabarain Tokyo, Japan|Akihabara]]===
Known as a mecca for videogame, manga, animation and hobby stuff. But it's not much in PoGo in spite of what one might expect. Nothing really special, there's a lot of better places to play PoGo in Tokyo.