Perched on a cliff overlooking the East China Sea, its rectangular white façade standing out in stark relief against the blue sky, Emil Nakijin is an ultra-modern boutique hotel with just five suites. They’re lined up in a row facing the ocean, with bright interiors that are nearly identical — minimalist and all-white — with nothing to distract from the spectacular surrounding landscape.

There’s a disproportionate number of lodging options on tiny Kouri Island — understandable, given its gorgeous natural scenery and quiet beaches on the emerald-green sea. The architecturally striking Yawn Yard, set on a forested hill overlooking the water, is among the best. This boutique hotel occupies a series of angular blonde-wood villas, all featuring private outdoor spaces with dining areas.

There’s only one museum in the world dedicated to the work of the American artist Keith Haring, and it’s not in New York. The acclaimed Japanese architect Atsushi Kitagawara designed the Nakamura Keith Haring Collection and the adjacent Hotel Keyforest Hokuto, both part of a larger art-themed resort. This boutique hotel is visually striking, its modernist silhouette and sharp angles standing out in contrast with the surrounding forest.

Walk past an imposing gate on an unassuming street and you’re suddenly surrounded by a sublime hush as you enter Yoshida Sanso’s historic main building. Built in 1932 for a member of the Japanese imperial family, the inn looks illustriously traditional at first glance, yet reveals restrained hints of modernism, such as the stained glass windows. All guestrooms in the main building come with a view of the expertly tended garden.

Bed and Craft provides the opportunity to not only stay in Nanto — a city with a proud heritage of woodworking — but to take up woodcarving. A collection of six historic buildings, from carpenter’s shop to restaurant, provide a place to rest and relax in a traditional Japanese environment. Guests are urged to embrace the opportunity to try their hands at carving their own keepsakes from a memorable getaway.

There’s a Ghibli-esque tranquility to the Hakone Geihinkan Rin-Poh-Ki-Ryu hotel. One arrives by cable car down steep, forested hillsides to its peaceful valley villas, lulled by the murmuring of the Hayakawa river. There are nine of them, each a strikingly original play on age-old Japanese materials like kumiko wood detailing, delicate paper screens, and gleaming lacquer. Some villas offer attached sauna and open-air hot springs.

It’s fair to say Ugenta, a two-room, 200-year-old ryokan in the mountain woods just outside Kyoto, isn’t exactly designed to maximize profits. Put it this way: they’ve got as many teahouses as they have guest rooms, one built a century ago by the current owner’s grandfather for formal tea ceremonies, and a newer, glass-walled one surrounded by a cedar grove for casual sipping.

Founded in 1911 in the sleepy city of Uwajima, Kiya has a long history of hosting Japanese literary figures, and more to the point for guests who don’t happen to be Japanese literary figures, it’s fresh off a very thorough restoration. The result is a clean, pared-down design, with traditional elements and modern details coexisting in a matter-of-fact way.

In Ryokan Kurashiki’s case, what most sets it apart is a location not in some tranquil middle of nowhere, but right in the heart of the historic merchant’s quarter of the city of Kurashiki. It’s the rare ryokan whose ability to transport guests back in time extends beyond its walls, helped along by the beautifully preserved 17th-century architecture of the neighborhood just beyond.

The forested mountains of Kagoshima Prefecture, by the side of the Amorigawa River, are the setting for the exquisitely traditional and uncommonly tranquil Gaojen. Here thatched roofs disappear into the forest canopy, and the sound of the river finds echoes in the inn’s carved-stone onsen baths. These rooms were the first in Japan to feature private onsen baths, either on wooden terraces or in semi-open spaces.

Between the mountains and the sea in Otake City, Hiroshima Prefecture, the futuristic complex that contains Simose Art Garden Villa was designed by the Pritzker winner Shigeru Ban and features a modern art museum, not one but ten villas, and a restaurant. Each villa is one of a kind, and some take inspiration from Japanese architectural landmarks.

Not a Hotel Fukuoka is a dynamic sequence of short-term residences, just eight in total, but also a series of vertical gardens and multi-use lifestyle hubs. The architects built it to transcend the divide between organic greenery and bold materials thinking. The “rooms” are enormous, each equipped with oversize windows, statement furnishings, and lighting that’s somehow both functional and experimental.

Yado Shiontei is just inland from the beach on Miho Bay in Yonago, Japan, an area renowned for high-quality timber and hot springs. Both are in evidence throughout the property, which blends traditionalism with sleek sustainability. There’s a lovely courtyard garden, an exquisite tea room, an art gallery dedicated to white porcelain, and a spa that can be privately rented with champagne service.

Staying overnight at Taniya, located in the historic castle town of Takayama, is akin to sleeping at Fallingwater or another architectural landmark. Positioned beside the Kusakabe Family Residence, an old merchant’s house designated an Important Cultural Property, this century-old two-room inn is an extension of its notable neighbor, both showcasing ancient Japanese techniques carried out by local craftsmen.

With just nine rooms, this wood-framed mountain retreat is ideal for those wanting somewhere cozy and snug. After a day’s skiing, the roaring fire in the lounge will be a welcome sight; in summer, if you’ve been hiking or horse riding, your aching bones will be grateful for the onsen. The bedrooms themselves at Kimamaya have a calming softness to induce a great night’s sleep, while the bistro is housed in an adjacent barn inspired by Hokkaido farm buildings.

Nasu Forest may be justly famous for the shrines and onsen and sake brewers, but don’t miss the trees for the forest. Nasu Mukunone Auberge lives this philosophy to its fullest. Beeches and cedars soar in the mountain breeze, weathered joists nod to local architectural heritage, and there’s even an expansive water garden on site for the world’s most transcendent stroll. This is a place of stillness and tranquil reveries.

The Japanese artist and hotelier Shouya Grigg is a collector — not only of art, but of architecture. For his latest project, Shiguchi, he relocated a series of kominka, or traditional wooden farmhouses, to a quiet valley outside the ski resort of Niseko. Their A-frame structures have remained more or less the same, but inside, they’re modern and minimalist, with private onsen baths, curated libraries, and terraces overlooking the surrounding landscape.

Zaborin is every inch a classic ryokan, from its unspoiled natural setting to the elaborate artistry of its kaiseki dinners. But it’s a thoroughly modern ryokan as well, and a modernist one at that — the architecture, by Makoto Nakayama, perfectly evokes the contemplative mood suggested by the name, which means something like “to sit and forget in the woods.” The woods in question are the forests of Hokkaido.

As Miyazaki-esque locales go, you can’t do much better than Niigata Prefecture, home to a sizable portion of the so-called Japanese Alps. Satoyama Jujo, sequestered deep within that enchanting mountainscape, blends eco-conscious boutique sensibilities with the region’s centuries-old kominka tradition: rural, wooden-frame homesteads designed to withstand harsh winters while remaining bright, clean, and tranquil.

As a name, Snow Peak Field Suite Spa Headquarters is a mouthful; Snow Peak is the upscale Japanese outdoor outfitter whose headquarters this is, and Field Suite Spa is the spectacular hotel on the site, designed by the master architect Kengo Kuma. The spa in question is an onsen-style spring-fed bath complex, which takes in panoramic views of its surroundings through full-length walls of glass.

Shoraiso’s name, meaning “wind through the trees in the mountains”, perfectly conjures the luxe onsen tranquility on offer here in the Nagano valley. A series of baths — indoor, outdoor, communal, private — comprise the main attraction here. There’s also a lounge bar with an attached garden for between-bathing breaks. Japanese-style rooms boast tatami, translucent screens, low-slung furnishings, and elegant details like arabesque archways.

Getting away from it all to connect with nature is the whole point of traveling to the remote Akan-Mashu National Park in Eastern Hokkaido, and there’s hardly a better place to do it than one of Wakkanpuri Resorts’ luxurious waterfront villas. Both are positioned on the edge of Lake Kussharo, the largest crater lake in Japan. Though they differ in style, both have minimalist living rooms warmed by wood-burning fireplaces and indoor baths fed by hot spring water.

A ski resort near Nagano may sound like an unlikely spot for a hotel dedicated to a Danish modernist architect. The furniture company Onecollection produces Danish-firm Finn Juhl’s designs in Japanese workshops, and its cofounders seized a chance opportunity to snap up an old ski lodge and reimagine it in his name. The result is a sleek six-room boutique hotel, House of Finn Juhl, with a striking blend of Japanese and Scandinavian elements.

It’s not hard to find Japanese hotels that aim to preserve tradition, but Wanoi Kakunodate takes it further than most — the Wanoi name, after all, is an archaic word for “Japanese way of life.” This collection of three old houses in the Akita prefecture aims for a time-travel experience, each one a meticulous preservation of its former use: a pickle storehouse, a fabric shop, and most improbably, a samurai’s residence.

The spectacular landscape of Niseko, in the shadow of Mount Yotei, is the backdrop for Raku Suisan, a modern interpretation of the timeless concept of the Japanese ryokan. The hotel’s rooms come in both tatami and Western varieties, and each one has its own private spring-fed onsen bath, on a terrace with a view of the landscape. Hokkaido is perhaps best known overseas as a winter-sports destination, but it’s a draw in all four seasons.

A glance at the distinctive silhouettes of Andaru Niseko’s villas and it’s clear you’re in for something unusual here. Architect Koichi Ishiguro was inspired by the traditional dwellings of the indigenous Ainu people, and if the end result has something in common with Alpine A-frames, it’s no accident — Niseko, on the island of Hokkaido, is a popular winter destination, and these two-story villas stand tall above even the deepest snowfall.

Tucked behind a decorative thatched-roof gate, Yamagata The Takinami occupies a centuries-old house built to withstand the region’s heavy snow. But instead of traditional tatami mats and tea rooms, its minimalist interiors feature sleek Nordic-style décor and modern Japanese design — a row of Arne Jacobsen’s Swan chairs line up beside big picture windows in the living room, while guest rooms feature pieces by Tendo Mokko.

TRUNK HOUSE is Tokyo’s most exclusive one-room stay, a painstakingly restored 70-year-old geisha house in the storied streets of Kagurazaka. Inside, tatami-lined tea rooms and an irori hearth sit alongside Stephen Kenn leather sofas, terrazzo floors, and a cypress-wood bath set beneath shunga art. The real showstopper is a hidden, soundproofed disco with neon lights, a stocked bar, and a dance floor made for impromptu revelry.