Japan’s beauty is drawing overwhelming crowds. Popular destinations including Kyoto, Tokyo, Osaka, and even Nara and Kanazawa are experiencing unprecedented overtourism. Fortunately for travelers, Japan is abundant in beautiful destinations. In the country’s quieter corners, you’ll find serene shrines, hidden sakura groves, and centuries-old onsen, while fifth-generation ryokan invite you to slow down, wrapped in soft cotton yukata robes in tatami mat rooms, and indulge in elaborate and seasonal kaiseki meals.
Afar’s latest Hotels We Love list highlights the retreats that will get you far from Japan’s megacities and tourist hubs. Spanning from Okinawa and Kyushu to Shikoku and Hokkaido, these 12 hotels will lead you to lesser-known cities and the peaceful inaka (countryside), where the true rhythm of Japan comes to life.
Auberge Yusura
- Location: Ise, Mie Prefecture, Central Honshu
- Why we love it: Tranquil pond-side villas, proximity to Ise’s local sites, and exquisite cuisine
- From $384
- Book now
At Auberge Yusura, a relaxed boutique ryokan in the coastal city of Ise, you can channel your inner haiku poet as you meditate and find inspiration in one of five pond-facing villas, each named after a tree. The guest bathrooms are stocked with locally made Mikimoto bath amenities and come with deep soaking tubs constructed of specialty Kiso cypress, while super comfortable Japanese futons or Simmons mattresses and soft cotton pajamas help guests sleep well. Yusura’s kaiseki meals are a highlight and include matsutake beef, plus abalone and lobster caught by Ise’s local female Ama divers. While Ise is famed for the Ise Shima shrine, Japan’s most sacred, the bayside Futamiokitama Shrine and the famous wedded rocks, tied together by a sacred rice straw rope, are only a short walk from the property.
Bettei Otozure
Bettie Otozure is located in the onsen town of Nagato, Japan.
Courtesy of Bettie Otozure
- Location: Nagato, Yamaguchi Prefecture, Honshu
- Why we love it: For its peaceful atmosphere by the river, and its selection of Western or traditional tatami mat rooms
- From $286, including dinner
- Book now
The serene and historic Bettei Otozure ryokan sits on a wooded bank of the Otozure River in the sacred onsen town of Nagato, two hours from bustling Fukuoka. The town is famed for its 600-year old alkaline Yumoto Onsen, where a shinto shrine stands within the bath. The property has its own garden, library, and grand outdoor bath and has even hosted Japan’s Emperor and Prime Minister. Its rooms, whether Western-style with hardwood floors or traditional tatami mat sanctuaries, all have private balcony onsen. The ryokan’s excellent restaurant serves Yamaguchi kaiseki, with specialties like fugu sashimi and minced lotus root with maitake and yuzu. Fifth-generation owner Kazuhiro Otani recommends pairing these with local sake or his personal favorite, mineral-forward Swiss wines, carefully selected for the ryokan’s cellar.
Daikokuya
In a less-visited part of Japan, Daikokuya offers an immersion in nature.
Photo by Shoko Takayasu
- Location: Nasu, Tochigi Prefecture, Honshu
- Why we love it: For a stay in the heart of Nasu’s natural beauty
- From $335
- Book now
There’s no shortage of elegant properties in woodsy Nasu, a 75-minute Shinkansen ride away from Tokyo Station and where the imperial Japanese family summers. The peaceful mountain town is home to ski resorts, forested cycling paths, and ancient onsen. But what truly sets Daikokuya apart are its unique outdoor art garden, a DIY ikebana station where guests can choose their own flowers and vases for their room’s tokonoma alcove, and a communal outdoor hearth and tea pavilion. Rooms come in three categories—ume, matsu, and take—and all have tatami mat floors, locally crafted furniture, and windows that open to a private garden or the flowing Nakagawa River. Onsen of both cypress and stone, and a relaxation room insulated with loess clay walls, help foster deeper tranquility, while in-house laundry machines are a welcome amenity for travelers on extended stays.
Horohoro Sanso
- Location: Date, Hokkaido
- Why we love it: A traditional ryokan near Mount Horohoro and shrine-dotted Lake Toya
- From $171
- Book now
There’s more to Hokkaido than powdery snow in Niseko and nightlife in Sapporo. In the Kitayuzawa Onsen district of Date, Horohoro Sanso is a traditional tatami mat ryokan with a steep gabled roof and charmingly creaky floors., It’s a relaxing retreat near Mount Horohoro and its circuits of hiking trails and the shrine-dotted shores of Lake Toya. The 154-room property has an indoor bedrock onsen, outdoor rotenburo (open-air baths), tennis court, putting green, sauna, and fitness classes. While buffets aren’t for everyone, the nightly spread here—included in the price—is elaborate and high quality, serving up crab legs, shabu shabu, onsen eggs, tempura, DIY hibachi grills, house-made tofu, and more.
Iraph Sui, a Luxury Collection Hotel
Iraph Sui is in the Miyako Islands of Okinawa, Japan.
Courtesy of Iraph Sui
- Location: Miyako, Okinawa
- Why we love it: A taste of Japan’s tropical side with cuisine that celebrates the island’s unique terroir
- From $1,108
- Book now
The 58 Western-style rooms at this airy beach resort on the island of Irabu, in Okinawa’s-lesser visited Miyako Islands, make for an ideal base while exploring Japan’s tropical side. The islands, known for their miles of secluded white-sand beaches, offshore fishing, snorkeling, and shimmering blue waters, are a sought-after escape for Japanese travelers looking to unplug from the country’s megacities. Iraph Sui, a Luxury Collection Hotel’s light-filled rooms, some with balconies and private plunge pools, are decorated in white and sea blue tones, while a gym, SUP yoga, on the sea or pool, and spa featuring mineral-rich kucha mud scrubs from the Okinawa seabed highlight this Blue Zone, famed for its residents’ longevity. Don’t miss Tin’in restaurant, serving French Okinawa fusion cuisine like fish tartare with marinated Okinawa vegetables, sautéed papaya with local bonito, and grilled Okinawa wagyu beef.
Kai Izumo
Kai Izumo’s Kagura, or ceremonial Shinto dances, are a nightly event.
Courtesy of Kai Izumo
- Location: Izumo, Shimane Prefecture, Honshu
- Why we love it: For its scenic ocean setting, intimate connection to local Shinto traditions, and exquisite seafood-forward kaiseki dining
- From $127, including dinner
- Book now
Set on a remote and windswept clifftop overlooking a chain of rocky islets in the Sea of Japan, Kai Izumo opened in 2022 and offers travelers a dreamy coastal getaway a 2.5-hour drive from the crowds of Hiroshima. Rooms, many with water views including the historic Hinomisaki Lighthouse, have tatami mats and pink and tangerine-hued washi wall art, a nod to the region’s legendary sunsets. (Some rooms come with private balcony onsen.) Guests are treated to nightly Kagura, ceremonial Shinto dances depicting the origin myth of the local Izumo Taisha Shrine, performed on the property’s sea-facing stage. But getting off property is easy too; just wander into the picturesque fishing village of Hinomisaki to visit the sea-weathered shrine crouched under centuries old cedar and camellia trees. Stays include elaborate kaiseki meals showcasing regional delicacies like Matsuba crab miso, local uni-topped sesame tofu, and Kobako crab gratin.
Kanran
Kanran is housed in a miniature farmhouse in Shikoku, Japan.
Courtesy of Kanran
- Location: Kagawa, Shikoku
- Why we love it: A slow-living retreat on the remote Sounai Peninsula
- From $202
- Book now
A miniature minka (farmhouse), Kanran is part of a constellation of rentals in the owner’s portfolio. It’s on a hillside olive tree farm on the Sounai Peninsula on a remote outcrop of Shikoku, not far from touristed Art Islands. The tree-house-like guesthouse overlooks the placid Seto Sea with wood walls and ceilings, lending it a cozy atmosphere. Rocking chairs and straw cushions invite guests to enjoy a slow morning by the floor-to-ceiling windows, which let in golden sunlight from the surrounding sea, while a wraparound outdoor deck is perfect for morning coffee and birdsong. Guests can sign up for udon cooking courses with the lodge’s food attendant, Maya, who will help you make Kagawa-style Uchikomo udon or use some of the local citrus and olive oil from the area.
Nipponia Sado
Nipponia Sado is in the town of Aikawa on Sado Island.
Courtesy of Nipponia Sado
- Location: Sado Island, Niigata prefecture, Honshu
- Why we love it: A thoughtful restoration of a historic warehouse with panoramic views of the Sea of Japan
- From $194
- Book now
In response to Japan’s growing number of abandoned and underused buildings, Nipponia Hotels specializes in transforming these forgotten spaces into boutique stays. One of its latest, Nipponia Sado, opened in the summer of 2024 in the sleepy town of Aikawa on Sado Island in the Sea of Japan, off the coast of Niigata. The area’s gold and silver mines were designated as UNESCO World Heritage sites in 2024, but Sado is known for its bioluminescent tub boat excursions, rice paddy bird-watching tours, and taiko drum performances. This hotel occupies a former storage warehouse, which has been carefully restored. Rooms have traditional Japanese design details like sliding shoji screens, washi paper lanterns, and tatami mat floors, alongside unique earthen walls. For breakfast, hike up the hill to the property’s café for sweeping views over the Sea of Japan.
Not a Hotel Aoshima
Not a Hotel Aoshima is on Aoshima Beach, popular with surfers.
Courtesy of Not a Hotel Aoshima
- Location: Aoshima, Miyazaki Prefecture, Kyushu
- Why we love it: For its exclusivity, island-inspired design, and warm hospitality of owners
- From $675
- Book now
The seafront Not a Hotel Aoshima sits on the popular surfer spot of Aoshima Beach. Its six units opened in late 2022, each with state-of-the-art technology like heated floors, built-in humidifiers, smart kitchens, and high-tech washers and dryers. But you can turn off the tech at outdoor firepits and hammocks and chill to the sound of waves. The spacious layout includes large living rooms ideal for groups or families, private terraces, some with outdoor soaking baths, saunas, barbecue grills, and pools overlooking the beach and the historic Aoshima shrine, enveloped by ancient and mossy tropical palm trees. The minibar is offers high-end goodies like rare Japanese whiskies and bottles of Miyazaki shochu, and reef-safe sunscreen, while beer, juice, soda, water are complimentary.
OMO5 Gotanda
OMO5 Gotanda has Tokyo skyline views from its guest rooms.
Courtesy of OMO5
- Location: Gotanda, Shinigawa, outskirts of Tokyo
- Why we love it: A different side of Tokyo in the city’s outskirts (with affordable rates)
- From $130
- Book now
Hoshino Resorts is known for its elegant Hoshinoya and culture-focused Kai properties. But the Japanese hotel group also maintains the affordable and design-forward OMO brand with tiers 3, 5, and 7 indicating the quality of each property. One of the newest, OMO5 Gotanda, opened in April 2024 in Gotanda, a neighborhood in Tokyo’s outskirts. Visitors who need a break from the relentless crowds of Shibuya and Shinjuku or who want to find a slice of tourist-free Tokyo will appreciate the emerging neighborhood, home to universities, the city’s largest meat market, and Sony’s new headquarters. Occupying the top floors (14th to 20th) of the Gotanda JP Building, the hotel has spacious tatami mat guest rooms that sleep up to four and offer uninterrupted views of the skyline; a large outdoor lounge, café, and coworking space, plus a 24/7 gym, make it ideal for digital nomads. A separate wing for dog owners includes a two-level dog park, DIY dog grooming sink and shampoo station, and a swanky photo staging area to take pics of your freshly coiffed pup.
Takasaki Stay
Takasaki Stay is an exclusive-use hotel on Goto Island, Japan
Courtesy of Takasaki Stay
- Location: Takasaki, Goto Islands, Nagasaki prefecture, Kyushu
- Why we love it: An exclusive-use retreat with inviting local owners with insider recommendations
- From $337
- Book now
Behind a seawall in the far-flung port town of Takasaki on Goto’s main island Fukue, Takasaki Stay is an exclusive-use, single-dwelling property that opened in 2024 and invites guests to embrace the island’s slower pace. Its English-speaking transplants from Tokyo are eager to help you explore the island’s emerald green hiking trails, solitary beaches, friendly izakaya, and UNESCO-listed Christian churches. Takasaki’s breezy interiors are decorated with cloud and wave themed washi shoji screens and shutters, modernist wicker furniture built by Nagasaki artisans, and watercolor landscapes of the island’s picturesque villages. In addition to a laundry machine and a deep soaking tub, the fully stocked self-catering kitchen lets guests prepare their own washoku (Japanese cuisine), although a local chef can be arranged if preferred.
Tocen Goshoboh
Tocen Goshoboh has been in operation for 15 generations.
Courtesy of Tocen Goshoboh
- Location: Arima Onsen, Hyogo Prefecture, Central Honshu
- Why we love it: For its salt-rich onsen, kaiseki dining, and idyllic alpine setting
- From $262
- Book now
This charming 15th-generation ryokan is just a scenic 12-minute ride from Kobe city on the Rokko-Arima Ropeway, a cable car that soars over the towering evergreens and cascading waterfalls of the steep Rokko Mountains. More than 800 years old, Tocen Goshoboh is renowned for its rare nonvolcanic salt–rich kinsen (gold colored) onsen. It’s fed by a mineral-rich subduction zone that has a salt concentration twice that of seawater and contains seven of the nine minerals officially designated by Japan as healing. Standout kaiseki meals include marbled Kobe wagyu sukiyaki, fresh sashimi from the nearby Kobe Port, and simmered dishes with sansho pepper, a local Arima speciality—best paired with locally brewed taruzake, aromatic sake aged in cedar casks.
