Written by Aarohi
Japan’s big-name destinations are busy for a reason, but they’re far from the whole story. Of the country’s 47 prefectures, some see only a fraction of the visitors that crowd into Tokyo, Kyoto and Osaka. But it’s not for a lack of things to do, sights to see, and bites to eat. Read on to find out about five prefectures worth visiting — plus one bonus island.
1. For mythology and mystery: Shimane Prefecture
Pro tip: Don’t skip the Horikawa Sightseeing Boat, which takes you around Matsue’s preserved townscape and allows you to hop on and off for a flat fee.
Shimane remains blissfully under-the-radar, but thanks to its combination of myth, mystery, and ancient history, we think that’s soon going to change.
Start with Izumo Taisha, one of Japan’s oldest and most atmospheric shrines. Associated with matchmaking, the enormous sacred rope — or shimenawa — is awe-inspiring. If you stay overnight in the area (which we recommend), you may see fireflies, deer, and other critters along the fringes of the satoyama.
From there, head to Matsue, home to one of Japan’s few surviving original castles, and take a scenic boat ride. Naniwa Issui (check rates), one of our top picks for accessible hotels in Japan, is also in Matsue — as is the former home of Lafcadio Hearn (known in Japan as Koizumi Yakumo), the writer who did much to bring Japanese folklore and ghost stories to readers around the world.
If you’re keen to hike, the far-flung Oki Islands, a UNESCO Global Geopark (of which Japan has 10 in total), are only a short plane ride away. We recommend basing yourself at Entō (check rates), an award-winning hotel that emphasizes sustainability.
How to get there
Japan Airlines (JAL) operates regular flights from Tokyo (Haneda) to Izumo. From Izumo Airport, catch an Airport Limousine Bus.
From Hiroshima or Okayama, trains make more sense.
2. For sweeping sand dunes and solitude: Tottori Prefecture
Pro tip: Get the San’in-Setouchi-Shikoku Expressway Pass if you plan to drive around Tottori and its surrounding areas (only available to non-Japanese passport holders or Japanese passport holders with permanent residency abroad).
Tottori is Japan’s least populous prefecture, and it often feels that way in the best possible sense. The big draw is the Tottori Sand Dunes, a sweep of wind-shaped sand by the Sea of Japan. Go early or late in the day for fewer people and better photos.
There’s more than sand dunes, though. The Uradome Coast has clear water, rocky inlets and boat tours, while Mt. Daisen offers hiking, temples and big mountain views without the crowds of better-known peaks.
Onsen fans can add Misasa Onsen, a traditional hot-spring town known for its radium-rich waters — the good kind.
There’s also a pleasingly odd pop-culture side to Tottori. Sakaiminato is linked to manga artist Shigeru Mizuki, creator of GeGeGe no Kitarō, while Hokuei abounds in Detective Conan references.
How to get there
All Nippon Airways (ANA) operates regular flights from Tokyo (Haneda) to Yonago Airport. As Tottori borders Shimane, you can also consider combining them into one trip — but make sure to spend at least one night in each prefecture so you’re not rushing.
3. For dinosaurs and crafts: Fukui Prefecture
Pro tip: For a traditional hot-spring stay with all the bells and whistles, stay at a ryokan (traditional inn) in Awara Onsen.
The Hokuriku Shinkansen now runs all the way to Fukui, making this small-but-mighty prefecture much easier to add to a Japan itinerary.
Fukui has become almost synonymous with dinosaurs, thanks to the renowned Fukui Prefectural Dinosaur Museum. Before you write it off as one for the kids, there’s a proper reason for the hype: the prefecture is one of Japan’s richest dinosaur fossil sites, and several species discovered there carry the Fukui name, including Fukuisaurus and Fukuiraptor.
If you want to skip the dino stuff, there’s still plenty to do. Make the pilgrimage to Eihei-ji Temple, a major center of Zen Buddhism founded in the 13th century, and check out the rugged basalt cliffs at Tōjinbō.
For crafts, Echizen is a must, where handmade paper, knives, and pottery have been made for centuries.
How to get there
Fukui is an easy add-on if you’re already visiting Kanazawa, with the bullet train taking only about 25 minutes between the two. From Tokyo Station, you can reach Fukui Station in just under three hours, and Awara Onsen is roughly another 30 minutes by local train. You can book Hokuriku Shinkansen tickets on Klook.
4. For mesmerizing natural scenery: Tokushima Prefecture
Pro tip: Slurp down on the local specialty of Handa sōmen, an especially bouncy type of noodle made without alkaline water or kansui (how do they do it?).
For a prefecture so tiny, Tokushima has a lot going for it: dance, mountain villages, whirlpools, and some of Japan’s most dramatic scenery.
The headline act is Awa Odori, Tokushima’s famous summer dance festival, when the city fills with performers and music. Outside festival season, you can learn about the dance at the Awa Odori Kaikan.
Near Naruto, the Naruto whirlpools churn beneath the bridge connecting Shikoku and Awaji Island. Inland, the Iya Valley is a true picture of “rural Japan”: vine bridges, steep mountains, river gorges and villages that feel a long way from the bullet-train map.
Tokushima is also part of the Shikoku 88 Temple Pilgrimage, so you’ll see white-clad pilgrims along the way.
How to get there
Tokushima works well as an entry point to Shikoku from Kansai, especially via bus from Osaka or Kobe. For a fuller trip, combine it with Kagawa or Kochi.
5. For hot springs and cozy vibes: Akita Prefecture
Pro tip: Stay near Akita Station, because accommodation options in Kakunodate are limited.
Most people know Akita for its namesake pooch — the famous, fiercely loyal Akita inu, immortalized by Hachikō. While the statue outside Shibuya Station is one of Tokyo’s busiest meeting spots, the prefecture is serene, and offers many a less-trodden path. If you like rustic, snow-blanketed hot springs and soul-warming stews and sake, look no further.
One of Akita’s popular spots is Kakunodate, a former samurai district known for its preserved residences and weeping cherry trees in spring. It’s one of the prettiest historic towns in northern Japan, but sees far fewer international visitors than similar spots like Kawagoe and Kamakura, both of which are near Tokyo.
For onsen, Nyūtō Onsen is the classic pick: a cluster of hot-spring inns tucked into the mountains near Lake Tazawa. And if you’re after something a little stranger, head to the Oga Peninsula, home of Namahage, fearsome folk figures who stomp into homes on New Year’s Eve to scare laziness out of children and adults alike.
How to get there
Akita works best as part of a Tōhoku trip with Aomori, Iwate or Yamagata. The consolidated JR East Pass, which offers unlimited travel across five or ten days (¥35,350 or ¥50,500), can be purchased online here.
Bonus — For sake and a taste of the slow life: Sado Island, Niigata Prefecture
Pro tip: You’ll need a car, as the main sights on the island are quite spread out and public transport is minimal.
Sado Island is a massive, wind-swept island that produces far more rice than its very few inhabitants consume.
While here, ride in the famous circular boats, try taiko drumming, and sample local seafood and sake. Obata Shuzo comes highly recommended — the family-run brewery uses local ingredients, including rice that is grown using a special oyster-shell farming method to provide nutrient-rich soil.
See if you can spot a crested ibis or toki, the region’s most iconic bird and a protected species.
How to get there
Sado Island is a ferry ride away from Niigata Port, which is located around a 20-minute bus ride from Niigata Station.
Frequently asked questions
How did we choose these prefectures?
We looked at official tourism data, then focused on prefectures that repeatedly appear near the lower end for visitor numbers, especially among international travelers. We also considered whether they make sense for independent travelers looking for quieter, practical alternatives to the usual route.
Which one is easiest to add to a first-time Japan itinerary?
Fukui is probably the easiest now, especially if you’re already visiting Kanazawa or traveling along the Hokuriku Shinkansen route. If you’re heading to Hiroshima, Shimane and Tottori are not far.
Which one is best for getting away from crowds?
For space and scenery, Tottori and Shimane are strong picks. For hot springs and a deeper rural feel, Akita is hard to beat — especially outside peak festival and cherry blossom periods.
