Millions pour into Tokyo and Kyoto every year, but the Japan most travelers miss exists on tiny islands scattered across the archipelago.
Picture volcanic rock hot springs submerged by high tide, olive groves on hillsides overlooking the Seto Inland Sea, and villages with just one traffic light serving 500 people.
These five lesser-known Japanese islands offer something the crowded tourist trail can’t.
Authenticity without the struggle to find it.
Iki Island, Nagasaki Prefecture
Tucked between Kyushu and South Korea, Iki Island combines dramatic coastal scenery with surprisingly easy access from mainland Japan.
A jetfoil ferry from Hakata Port in Fukuoka takes about an hour.
Direct flights from Fukuoka or Nagasaki airports land in just 30 minutes on small propeller planes.
The island’s main attraction is the emerald water around Tatsunoshima.
This tiny islet is just a 40-minute boat ride from Katsumoto Port. Tours run from March to November.
The clarity of the sea here rivals anywhere in the Seto Inland Sea, making it popular with snorkellers despite relatively cool water temperatures.
Beyond the beaches, Iki offers natural hot springs scattered across the island, many with ocean views.
The local economy focuses on fishing and barley farming.
You’ll see the island’s unique shochu distilleries scattered throughout the interior.
Iki has a population of fewer than 27,000 people spread over 134 square kilometres.
It feels remote, but it’s still practical for independent travel.
Shikinejima, Tokyo
This volcanic speck in the Izu Islands sits just 160 kilometres south of Tokyo, reachable in three hours aboard a high-speed jetfoil from Takeshiba Pier.
Despite falling within Tokyo’s administrative boundaries, Shikinejima feels like a different country entirely.
The island measures only eight square kilometres and has a single traffic light serving its 500 residents.
Most visitors explore on foot or rent bicycles from the small shop near the port.
A coastal walking trail goes around the whole island in about four hours.
It takes you through camellia trees and shows off sharp lava formations.
Shikinejima’s main draw is its collection of free outdoor hot springs built directly into the coastline.
The most famous, Jinata Onsen, sits carved into black volcanic rock at the water’s edge.
Timing matters here because high tide submerges the pools, making them unusable.
Check the tide tables posted at the port before planning your soak.
Accommodation options are limited to a handful of minshuku guesthouses and one small hotel.
Book well ahead during summer weekends, when Tokyo residents escape the city heat.
The island has no convenience stores, so bring cash and any supplies you might need.
Shodoshima, Kagawa Prefecture
Japan’s olive oil production started on Shodoshima in 1908.
The island still grows nearly all of the country’s domestic olive harvest.
The climate here is great for olives and citrus groves.
It also hosts over 400 soy sauce breweries, some of which are centuries old.
Ferry services connect Shodoshima to multiple ports on Honshu, with the most frequent departures from Takamatsu taking about an hour.
The island spans 153 square kilometres, making a rental car or scooter practically essential unless you stick to the main towns.
Kankakei Gorge runs through the mountains.
It has hiking trails and a ropeway that rises 612 metres. From the top, you can enjoy stunning views of the Seto Inland Sea.
Autumn changes the gorge into one of Shikoku’s most photographed places.
The maples turn bright red next to the grey rock walls.
Every three years since 2010, Shodoshima has hosted the Setouchi Triennale art festival.
Permanent installations remain visible year-round, including works scattered along the coast and in abandoned villages.
The most accessible pieces cluster around Tonosho Port, where ferries arrive.
The island’s beaches lack the tropical warmth of Okinawa but offer calm swimming conditions and fewer visitors than mainland resorts.
Angel Road is a sandbar that shows up at low tide.
It links small offshore islands and attracts crowds for sunset photos. It’s only about 500 metres long.
Kurima Island, Okinawa Prefecture
Connected to Miyakojima by a 1,690-metre bridge, Kurima Island offers a gentler introduction to remote island life than most destinations on this list.
The bridge opened in 1995, making the island accessible by car in just 15 minutes from Miyako Airport.
Despite this convenience, Kurima maintains an authentic rural atmosphere with only around 200 permanent residents.
The island measures nine kilometres in circumference, small enough to explore in 10 minutes by car or 30 minutes by bicycle.
Sugarcane fields dominate the landscape, interrupted only by a small village on the eastern side.
Unlike many tourist destinations, Kurima has avoided heavy development whilst embracing selective modernisation through trendy cafes and boutique shops selling handmade crafts.
Musunun is a stunning beach hidden one to the south, and it’s really more of a scenic/cultural spot than a swimming beach.
The beach receives few visitors and lacks any facilities, making it ideal for sunset viewing in complete solitude.
Ryugujo Observatory, styled after a mythical underwater palace, rises three storeys above the island’s highest point.
From here, you can see the entire island, Kurima Bridge, and neighbouring Yonaha Maehama Beach.
Direct flights from Tokyo reach Miyako Airport in about three hours, with connections from Osaka taking roughly two and a half hours.
From the airport, Kurima Bridge is just a 15-minute drive.
Most visitors treat Kurima as a day trip from Miyakojima, though one small guesthouse and a boutique hotel accommodate those wanting to stay overnight.
The island’s cafe scene has grown recently, with establishments like AOSORA PARLOR serving tropical smoothies made from locally harvested mangoes and other fruits.
These cafes often have queues during weekends, so arrive early or visit on weekdays.
Most accept only cash, and there are no typical convenience stores on the island.
Amami Oshima, Kagoshima Prefecture
Amami Oshima sits roughly halfway between Kyushu and Okinawa, blending subtropical forests with cultural influences from both regions.
In 2021, UNESCO recognised the island as part of a World Heritage Site protecting endemic species found nowhere else on Earth.
The island covers 712 square kilometres and has Japan’s second-largest mangrove forest.
You can best explore it by kayaking through its narrow waterways.
Several tour operators near the village of Sumiyou offer guided trips lasting two to three hours.
Between April and June, you might spot firefly squid glowing in the shallow channels after dark.
Two endangered species draw wildlife enthusiasts here.
The Amami rabbit, a primitive species with short ears and legs, appears on night drives along forest roads.
The Lidth’s jay, a striking blue and maroon bird endemic to these islands, calls from the canopy throughout the day.
Both animals face threats from introduced mongoose populations, though recent control efforts show positive results.
Direct flights from Tokyo, Osaka, and Fukuoka reach Amami Airport in 90 minutes to two hours.
No trains operate on the island, and bus service runs infrequently outside main routes, making car rental the practical choice for exploration.
Local cuisine centres on keihan, a chicken and rice dish served with a rich broth poured over the top, developed here during the Ryukyu Kingdom era.
Amami also produces kokuto shochu, a spirit distilled from brown sugar rather than the usual grain or sweet potato base.
Taketomi Island, Okinawa Prefecture
Just ten minutes by ferry from Ishigaki, Taketomi showcases a vibrant slice of traditional Ryukyu village life.
It spans 5.4 square kilometres.
Red-tiled roofs, coral stone walls, and white sand paths define the settlement, which houses only 360 permanent residents.
The island government enforces strict building codes to maintain this appearance, prohibiting modern construction materials in the village centre.
Stone walls must use local coral, whilst roof tiles follow historical patterns.
Walking through feels very genuine.
The rules help new buildings fit in with those that are over a hundred years old.
Kondoi Beach on the west coast offers Taketomi’s best swimming, with shallow turquoise water protected by an offshore reef.
The sand here contains tiny star-shaped grains formed from the skeletons of foraminifera, visible if you look closely.
Kaiji Beach on the east side produces better examples but strong currents make swimming dangerous.
Water buffalo carts are a key part of the Taketomi experience.
They move slowly through the village, and drivers sing traditional Okinawan songs.
Tours last about 30 minutes and cost around 1,200 yen per person.
Bicycle rental gives you more freedom, but since the island is small, you can see everything on foot in half a day.
No accommodation exists on Taketomi itself beyond one small guesthouse, pushing most visitors to treat it as a day trip from Ishigaki.
The last ferry back typically departs around 5:30 pm, with slight variations by season.
Arrive early to avoid tour groups that flood the village between 10 am and 2 pm.
Frequently Asked Questions About Japan’s Lesser-Known Islands
Shikinejima remains the most accessible by ferry, reaching the island in about three hours. However, Kurima Island offers the easiest overall access since you can fly to Miyako Airport from Tokyo in three hours, then drive across the bridge in 15 minutes.
Not necessarily. You can reach Shikinejima, Shodoshima, and Taketomi by ferry. Iki Island, Amami Oshima, and Kurima Island (via Miyakojima) are most practical to reach by short flights from major airports like Fukuoka, Osaka, and Tokyo.
Late spring and early autumn bring warm weather and fewer crowds. Summer is great for swimming and festivals, but accommodation books up quickly.
Yes. Each one offers good infrastructure, small guesthouses, and friendly locals. They’re less crowded than major tourist spots but still easy to navigate.
One to two days is ideal for smaller islands like Shikinejima, Kurima and Taketomi. Amami Oshima and Shodoshima deserve at least four days if you want to explore their nature and culture in depth.
