Are there local micro-breweries in Tokyo?
Are they serving local Japanese craft beer?
What are Japanese craft beer that one can find in Tokyo?
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There are many craft beer pubs in Tokyo. But there is no craft beer brand made in Tokyo. I recommend Coedo Beer from Kawagoe-city, Saitama-Pref.
Kawagoe is a traditional town near Tokyo. It takes 40 minutes by train from Shinjuku/Ikebykuro. Coedo has 4 flavors, "Kyara" (Golden Brown), "Ruri" (Blue), "Shiro" (White), "Shikkoku" (Black) and "Beniaka" (Red). Especially, "Beniaka" is made from sweet potatoes in Kawagoe. Kawagoe is famous for sweet potatoes.
And "Coedo" means "Little Edo". "Edo" is the old name of Tokyo. Kawagoe has still old Tokyo street.
Please come and drink up!
You can find a lot of different bars that sell micro-brews in Tokyo.
most All of the micro-breweries I know of are located outside of Tokyo. However, I can't definitely say "there are no micro-breweries in Tokyo" as I am not omnipotent.
Again, there are a ton of places to get micro-brews in Tokyo; here is a restaurant that I have frequented over the past years that serves Japanese micro-brews exclusively: BanKan.
BanKan has 14 taps of Japanese micro-brews and they rotate their offering frequently; whenever a keg runs out it is replaced with a new brew. A pint runs between 900 to 1400 yen and the current offering is here. Notice that the prefecture the brew comes from is listed as well.
On my 2nd trip to Tokyo, I found Popeye pub in a quaint part of the city @ Ryogoku: Popeye Beer Club.
They have 70 taps and mostly from Japanese breweries.
Another one is Ryujin Shuzo Brewery or Ginko Kura Brewery, from Gunnma Prefecture, not too far from the capital. Oze no Yukidoke IPA (that I tasted) seems to be their most popular product. I am disappointed for not finding any more precise references online now, but I advise to search the names in bold above on Google or Instagram (where I have my beer-also blog) to find some further pictures and information.