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Yutorelo Atami is a lovely boutique hotel that offers ocean views, excellent service, delicious meals, and boasts a wonderful open-air hot springs bath.
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.
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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. 
Shirakawa-go no Yu, a wonderful, convenient, ryokan in the downtown of Shirkawa-go, a UNESCO world heritage site.
Relax in your seaside room or in the ocean front onsen and enjoy delicious local seafood at Hagi Komachi in northern Yamaguchi Prefecture.
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!
If you are looking for a unique experience in an exceptional setting, look no further than Kaniyu Onsen. This ryokan hidden deep in the mountains of Oku-Nikko is well worth the trek to get there. Experience the regional countryside fare, hike through the forests, gain a deeper understanding of the local history, and of course, relax in one of the best onsens in Japan.
A Stay at the Kazeya Ryokan, a traditional Japanese inn in the heart of Gifu's Hida Mountain Range.