Japan’s serene, spiritual landscapes have inspired poets and painters for centuries. It might be famous for its ultra-modern cities, but beyond the urban sprawl, it’s blessed with natural scenery that sometimes seems so impossibly perfect it might as well have been dreamt up for a Miyazaki movie. From exploring the country’s secluded gorges and mirror-like lakes to quaint hot-spring towns and remote islands, adventurous travellers will be rewarded with a side of Japan that every visitor secretly craves but few get to experience. Several of these sights are little-visited by non-Japanese people, and if you pick your season carefully, they can be delightfully free of crowds.

Inevitably, the further you deviate from the main tourist route of Tokyo-Kyoto-Osaka, the wilder and emptier the country gets. For proper seclusion, head south to the tiny island chains around Okinawa, or travel to the northern island of Hokkaido, home to vast, wild national parks and epic hiking trails. Here are some of the best lesser-known beauty spots to enjoy.

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1. Oirase Gorge, Aomori prefectureOirase Gorge, Aomori prefecture — one of the most beautiful places to visit in Japan

Autumn colours in Oirase Gorge

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Way up at the northern end of Honshu island, about 90 minutes inland from the port city of Aomori, this dramatic nine-mile gorge looks like a scene from a Hokusai woodblock painting. Falling within the boundaries of Towada-Hachimantai National Park, the gorge is home to some of Japan’s loveliest beech forest, with carpets of moss, riverside trails and clattering waterfalls endowed with impossibly poetic names such as White Silk and Two Dragons. It’s a great area for hiking, especially in autumn for the forest colour. Nearby Lake Towada is also well worth a visit — a great caldera left behind by volcanic eruptions from long ago, it’s spotted with Shinto shrines and scenic lookout points.

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Rooms at the Towada Prince Hotel come with lake or mountain views, and there are grassy grounds and a piping hot onsen to try.

Heritage Expeditions’ 16-day cruise circumnavigation includes a stop about halfway into the journey to experience Lake Towada.

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2. Kenrokuen, Ishikawa prefectureA garden in Kenrokuen, Ishikawa prefecture — one of the most beautiful places to visit in Japan

Japan is a paradise for garden lovers, but there are three “Great Gardens” that represent the pinnacle of Japanese horticulture: Korakuen in Okayama, Kairakuen in Mito and Kenrokuen. This garden in the centre of Kanazawa is said to epitomise the six tenets of classical garden design: antiquity, artifice, spaciousness, seclusion, water and panoramic views. Originally the garden was a private pleasure ground that belonged to nearby Kanazawa Castle and could only be enjoyed by the ruling Maeda clan. It was opened to the public in the 1870s and is now famous for its pretty ponds, pathways, fountains and decorative features, such as the famous Kotoji Toro stone lantern. Come in early spring for the ume (plum blossom) show.

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Hotel Ao Kanazawa is a stylish hotel that’s less than a five-minute walk from Kenrokuen.

Kanazawa is a stop on Brightwater Holidays’ 14-day tour around the great gardens of Honshu and Hokkaido.

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3. Kinosaki Onsen, Hyogo prefectureKinosaki Onsen, Hyogo prefecture — one of the most beautiful places to visit in Japan

Cherry blossom season in Kinosaki Onsen

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After a devastating 1925 earthquake, the residents of Kinosaki Onsen worked together to rebuild the town as it was, with wooden buildings lining the willow-draped canals. The community takes just as much pride in maintaining the picture-perfect townscape now. Each evening guests staying in the traditional ryokan inns stroll along the streets in their yukata cotton kimonos, going “hot-spring hopping” between the many public baths. It’s a cosy scene, with steam wafting from the baths, herons perching in the canals and the click-clack of geta (wooden sandals) through the quiet streets.

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Nishimuraya Honkan is one of the best ryokan in Kinosaki, with hot springs, multi-course kaiseki cuisine and traditional hospitality. Public bath passes are included.

Inside Japan’s 11-night Hotsprings Honeymoon itinerary includes a stay in Kinosaki.

4. Taketomi Island, Okinawa prefectureKondoi beach on Taketomi — one of the most beautiful places in Japan

Kondoi beach in Taketomi

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In a far-flung part of the already far-flung Okinawan archipelago, subtropical Taketomi feels like its own little world. The tiny island — less than two miles wide — is home to about 300 people who live in a village of small houses with sloping, terracotta-tiled roofs and surrounded by rustic stone walls garlanded with flowers. Spend the day cycling to beaches with star-shaped sand or diving down to an undersea hot spring, then watch the stars come out as the balmy evening turns to a bright, clear night.

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You can stay in a classic Taketomi-style villa with red-tiled roof at the small Guest House Cago, conveniently located in the village at the heart of the island.

G Adventures’ 21-day Absolute Active Japan trip includes a day exploring Taketomi by bike.

• The best Japanese islands to visit

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5. Nikko, Tochigi prefectureToshogo shrine in Nikko — one of the most beautiful places in Japan

Toshogu Shrine in Nikko

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In the mountains north of Tokyo, Nikko combines a striking natural setting with elegant and historic shrines and temples. Chief among them is the ornate Toshogu, where each building is adorned with complex, brightly painted wood carvings by the best 17th-century artisans. One of the most popular carvings is a sweet depiction of a dozing cat above a doorway; pass through it and you’ll find steps to a simple stone monument with pine trees leaning protectively over it — the mausoleum of Tokugawa Ieyasu, the first Tokugawa shogun and one of the country’s Three Great Unifiers.

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Nikko Kanaya Hotel has an ideal location near Shinkyo Bridge and retains much of its historic grandeur.

There’s an overnight stay in Nikko on the eight-day Highlights of Japan tour from Exodus Adventure Travels.

• Best things to do in Japan

6. Akan-Mashu National Park, Hokkaido prefectureA whooper swan on Lake Kussharo in Akan-Mashu National Park— one of the most beautiful places in Japan

A whooper swan on Lake Kussharo

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In the wild, wide-open spaces of eastern Hokkaido — the northernmost of the four main Japanese islands — are three breathtakingly lovely lakes. The largest is Kussharo, where each winter whooper swans cluster in the few ice-free spots near the shore created by hot springs. Next is Mashu, a startlingly blue crater lake with some of the clearest water in the world. The delicate ecological balance of the smallest lake, Akan, produces marimo — bright green balls of algae that are celebrated in the torchlit Marimo Festival held by the indigenous Ainu people each October.

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Luxurious Akan Tsuruga Bessou Hinanoza has views over the lake, indoor and outdoor onsen, and some beautiful Ainu wood carvings.

G Adventures’ nine-day Active Japan: Hokkaido Adventure includes stops at viewpoints over lakes Kussharo and Mashu and an overnight stay near Lake Akan.

• Best time to visit Japan: when to go and what to do

7. The Iya Valley, Tokushima prefectureThe Iya Valley in Shikoku — one of the most beautiful places in Japan

The Iya Valley in Shikoku

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With its cloud-shrouded mountains, vertiginous ravines and deep forests, the Iya Valley on the island of Shikoku has a mysterious air. Its remoteness made it the perfect hideaway for the remains of the Taira samurai clan who fled here after their defeat in the Genpei War (1180–85), developing a unique culture in this secluded valley. Traces of the old ways of life are still present, from centuries-old thatched farmhouses to the vine bridges allegedly created by the Taira — they could be easily cut down, sending pursuing Minamoto warriors crashing into the river below.

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A stay at Hotel Iyaonsen combines a spectacular mountain location, sweeping views of the valley, soothing hot springs and delicious traditional food.

You can call a farmhouse in the Iya Valley home for two nights on Inside Japan’s Secrets of Shikoku trip.

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• The best tours of Japan

8. Yufuin Onsen, Oita prefectureKinrin Lake in Yufuin Onsen, Oita prefecture — one of the most beautiful places to visit in Japan

Kinrin Lake in Yufuin

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In a serene rural location, surrounded by rice paddies and mountains in eastern Kyushu, Yufuin Onsen is one of the prettiest hot-spring towns in Japan. Unusually its ryokan are dotted around, away from the centre (which is instead full of cute cafés and interesting museums), giving them a sense of calm and privacy. Each season has distinctive charms in Yufuin. On winter mornings, mist rises from the river that snakes through town and Mount Yufu is delicately dusted with snow. By summer, town and mountain are lush with greenery and the drone of cicadas drifts lazily on the air.

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In a quiet spot amid rice fields, Hoshino Resorts KAI Yufuin is a chic and comfortable retreat with spa treatments and hot-spring baths.

YellowWood Adventures has an eight-day tour around Kyushu, including stops to see Nagasaki, the Tenmangu shrine in Dazaifu, Sakurajima volcano, and a soothing day soaking in Yufuin Onsen.

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9. Hiraizumi, Iwate prefectureA temple in Hiraizumi — one of the most beautiful places to visit in Japan

Chusonji temple in Hiraizumi

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Though it’s now a sleepy historic town, in the 12th-century Hiraizumi was the northern headquarters of the powerful Fujiwara clan, and some treasures from that time still exist. For example, there’s Chusonji, a temple where you can walk along avenues lined with centuries-old trees and admire the Konjikido, a hall covered in gold leaf. At Motsuji, people in Fujiwara-style court dress compose poetry at the Gokusui no En festival in May and some 30,000 irises bloom each June. And west of town you can marvel at Takkoku-no-iwaya, an ancient temple built into a cliff face.

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Also to the west of town, Soba-an Shizukatei is a quiet and welcoming hot-spring inn serving up handmade soba noodles and vegetables grown in the kitchen garden.

Wendy Wu’s 14-day Journey Through Japan tour includes a stop in Hiraizumi.

10. Fuji Five Lakes, Yamanashi prefectureKawaguchi Lake with Mount Fuji in the background - one of the most beautiful places to visit in Japan

Lake Kawaguchi and Mount Fuji

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Mount Fuji has inspired Japanese artists and writers for as long as they have been there to see it, and it remains a powerful symbol of the country. The serene symmetry of the volcano is interrupted by a small second crater, which gives it a charming wabi-sabi quality — the Japanese concept of beauty in imperfection — and the surrounding Fuji Five Lakes area gives you plenty of good vantage points. One of the most famous of these lakes is Kawaguchi, which is easily accessible. When the leaves change colour each autumn, the Momiji Tunnel — a spot on the north shore — perfectly frames the snow-capped peak in reds and golds.

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In a wooded area near Lake Kawaguchi, Hanz Outdoor Resort has private villas and geometric dome tents called Pao — and, of course, Mount Fuji views.

The 16-day Japan Unveiled tour from Newmarket Holidays includes a visit to Lake Kawaguchi, and views of the mountain from Lake Ashinoko in Hakone.

11. Hagi, Yamaguchi prefectureThe town of Hagi, Horiuchi district, Yamaguchi Prefecture — one of the most beautiful places to visit in Japan

The Edo-period town of Hagi

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In a country prone to earthquakes, Hagi is a remarkably unspoilt historic town in western Japan. Its castle may have been destroyed in the 19th century — leaving behind a lovely coastal park ideal for walking and cycling — but the surrounding district offers a glimpse into everyday life when it was still standing. Stroll its streets and you’ll see the stern black and white walls of samurai mansions, wooden buildings that served as shops and inns, and the distinctively latticed plasterwork of former storehouses that are now museums, shops and restaurants.

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Hagi no Yado Tomoe puts an elegant, modern twist on traditional Japanese aesthetics — the raked gravel garden is particularly lovely.

You can experience a homestay and cycling in Hagi on G Adventures’ 11-day Back Roads of Japan trip.

12. Yakushima, Kagoshima prefectureAncient cedars on Yakushima Island — one of the most beautiful places in Japan

Ancient cedars at a forest in Yakushima

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It may look tiny on a map — just a drop of ink below Kyushu — but Yakushima feels huge. Several of the highest mountains in Kyushu are all on this island, their rocky slopes descending into a thick tangle of rainforest, which finally thins out into fruit orchards, fishing towns and white-sand beaches where sea turtles nest. The misty forests are the real draw, with several towering cedar trees that have been growing for thousands of years hidden in their depths. It’s a place where you can step back through time, connecting with deep history and truly wild nature.

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Sankara Hotel & Spa is a tranquil escape in southeastern Yakushima, with relaxing wellness treatments and sea views from every room.

YellowWood Adventures’ 11-day Lost Islands of Japan tour includes two nights on Yakushima.

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We regularly reassess and refresh this list, adding the latest advice and inspiration

What’s the most beautiful place you’ve been to in Japan? Please share in the comments below

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