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Taiyo no Sato: Bettei Umi to Mori was voted Japan's number one high end ryokan in 2014. Located just a couple of hours East of Tokyo along the most Eastern shores of Chiba prefecture, it offers delicious local seafood with private baths facing the Pacific Ocean.
Shirakawa-go no Yu, a wonderful, convenient, ryokan in the downtown of Shirkawa-go, a UNESCO world heritage site.
Nothing beats a long day exploring the classic wooden architecture of Narai. Unless its staying in one of its oldest and most well preserved ryokans!
A Stay at the Kazeya Ryokan, a traditional Japanese inn in the heart of Gifu's Hida Mountain Range.
Auberge Watanabe in Miyajima is conveniently located right in front of the entrance to the Daisho-in Temple grounds, on a quiet side street next to a stream.
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A popular onsen spot near Tokyo is the Nikko area in Tochigi prefecture such as the Kinugawa onsen. Located two hours from Tokyo, it is easily accessible by bus or train with JR or Tobu line. Kinugawa Park Hotels are one of the best hotels in this area to enjoy an unforgettable week-end with delicious food and amazing facilities. 
If you can manage to tear yourself out of the glorious onsen at KAI Matsumoto, why not check out the nearby Matsumoto castle?
This luxurious century old ryokan is home from Nobel Laureates to honeymooners alike. Calm and stately this is a perfect home away from home