Anime Goods Stores in Tokyo

This is just a listing of anime stores I know about in Tokyo by district / landmark.  It is a list that will likely be updated over time as I find new things or have to remove defunct stores.  I drew this list up for my own research so I hope it is of use to you.
  • Animate
  • Yodobashi Camera
  • Artnia Square Enix Cafe and a small shop (a bit of a walk on foot - take train)
  • Toho Building (where the giant Godzilla head is) now has a Godzilla store on the main floor (as of Oct 30, 2017).
  • Mandarake
  • Animate
  • Namco Character Shop  in Parco Part 1 (temporary closure for renovations in 2016?)
  • One Piece Mugiwara Store in Parco Part 1 (temporary closure for renovations in 2016?)
  • Production IG Store on the 7th floor of Shibuya Marui
  • One Piece Mugiwara Store on the 7th floor of Shibuya Marui
  • Loft
  • Tokyu Hands
Tokyo Tower
  • One Piece Theme Park
Tokyo Station
  • Character Street - many anime stores including Pokemon Center, Jump Store, Gundam Cafe, and Ultraman.  The stores tend to be small, but there are many of them.
  • Donguri Garden Store for Studio Ghibli character goods
  • Noitamina Goods Store in the Aqua City Mall
  • Fuji TV Store in the Fuji TV Building
  • Gundam Base Tokyo in Diver City (Gunpla kits) +  Giant Gundam out front.
  • Some character goods stores for Sanrio and even Chicken Ramen on the main floor Diver City
  • Toy R Us at Decks Mall
  • Donguri Garden Stores for Studio Ghibli character goods at Venus Fort Mall 
  • Cool retro shops and Showa theme park in Aqua City too.
  • Anime goods everywhere - you're in Akihabara
  • Gamers
  • Animate
  • Mandarake
  • Yodobashi Flagship Store Camera
  • Kotobukiya Store
  • Akiba Culture Zone (Good Smile Cafe on top floor)
  • New Radio Kaikan 
  • Square Enix Cafe and small shop.
  • Gundam Cafe and small shop.
Tokyo Skytree
  • Pokemon Center
  • NHK TV Character Store
  • Jump Store
  • Donguri Kyowakoku Store for Studio Ghibli character goods (giant Totoro in window display)
  • Hello Kitty Store
Nakano Broadway
  • Anime stores part of the mall has tons of stuff that is new and used.
  • Very cool Mandarake collectors store (expensive collectibles)
Ghibli Museum 
  • Museum shop has unique Ghibli items you won't find elsewhere.
  • Yamashiroya - cool toy store.
Omotesando / Harajuku
  • Kiddyland - more of generally amazing toy store.  Almost everyone sees something they want.
  • First permanent Sailor Moon store in Harajuku
  • Sanrio Store - pretty big one

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